# HG changeset patch # User iarc # Date 1461921088 14400 # Node ID 916846f73e25ab3420f92d020f351676ca8f0f74 # Parent 14fe7238c6d702737f6c995954702a26a20a0a00 Uploaded diff -r 14fe7238c6d7 -r 916846f73e25 Frequency-COSMICv72-Hupki-Others.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Frequency-COSMICv72-Hupki-Others.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,97 @@ +Substitution Type Trinucleotide Somatic Mutation Type Signature 1 Signature 2 Signature 3 Signature 4 Signature 5 Signature 6 Signature 7 Signature 8 Signature 9 Signature 10 Signature 11 Signature 12 Signature 13 Signature 14 Signature 15 Signature 16 Signature 17 Signature 18 Signature 19 Signature 20 Signature 21 Signature 22 Signature 23 Signature 24 Signature 25 Signature 26 Signature 27 Signature 28 Signature 29 Signature 30 Signature 1 MEF Signature 2 MEF Signature 3 MEF Signature 5 MEF Signature DMBA Signature MNU Signature Urethane +C>A ACA A[C>A]A 0.0110983262 0.0006827082 0.0221723068 0.0365 0.0149415477 0.0017 0.0004 0.0367180038 0.012 0.0007 0.0002 0.0077 0.0003347572 0.0001 0.0013 0.0161 0.0018320192 0.0505364186 0.0107 0.0011799616 0.0001 0.0015040704 0.0004533607 0.0286459925 0.009896768 0.0020397729 0.0052056269 0.0013974388 0.0699819873 0 0.000781083 0.0037229109 0.0283533537 0.0003710632 0.0121138158 0.0010972115 0.0044388346 +C>A ACC A[C>A]C 0.0091493407 0.0006191072 0.0178716754 0.0309 0.008960918 0.0028 0.0005 0.0332457222 0.0067 0.001 0.001 0.0047 0.0006487361 0.0042 0.004 0.0097 0.0003422356 0.0109398248 0.0074 0.0022115051 0.0007 0.002451011 0.0003668005 0.0202146384 0.0069989288 0.0014871623 0.0047382274 0.0009171877 0.0551523572 0 0.0022972224 0.0070460466 0.015676074 0.001672691 0.0046539767 0.0009508214 0.0004001609 +C>A ACG A[C>A]G 0.0014900705 0.000099279 0.0021383396 0.0183 0.002207846 0.0005 0 0.0025253113 0.0005 0.0003 0 0.0017 3.8144594E-005 0.0005 0 0.0022 1.576225E-006 0.0022880727 0.0005 1.61691E-007 0 0 0 0.0204789965 0.001448443 0.0002839456 0.0007826979 0 0.017846984 0.0019673 0.0031701397 0.0025537924 0.0272331284 0.0007812591 0.0071227909 0.0003972991 1.63618104265282E-020 +C>A ACT A[C>A]T 0.0062338852 0.0003238914 0.0162651456 0.0243 0.0092069053 0.0019 0.0004 0.0335985495 0.0068 0.0092 0.0002 0.0046 0.0008466585 0.0296 0.0057 0.0088 0.0031796648 0.0194240914 0.0074 0.00300801 0.0006 0.0009224525 0 0.0246001454 0.004966565 0.0005978656 0.0027182425 0.00051341 0.026804716 0 0.0015620621 0.0104484061 0.0079498813 0.0004287024 0.0083172408 0.0002539234 0.0015287933 +C>A CCA C[C>A]A 0.0065958701 0.000677445 0.0187817256 0.0461 0.0096749043 0.0101 0.0012 0.0317237566 0.0098 0.0031 0.0007 0.0135 0.0017100896 0.0056 0.0106 0.0159 0.0010324302 0.0887681088 0.0112 0.0173771106 0.002 0.0045496929 0.0001647394 0.0635592838 0.0148329479 0.0037058501 0.0050650733 0.0011685156 0.0514102117 0 0.0094052338 0.0035222831 0.0414403498 0.0050521059 0.0224513894 0.0008540231 0.0031599431 +C>A CCC C[C>A]C 0.0073423678 0.000213681 0.0157604578 0.0614 0.0049523006 0.0241 0.0006 0.0255054071 0.0057 0.0009 0.0017 0.0112 0.0011592566 0.0102 0.0084 0.01 0.0004218801 0.0206413906 0.0159 0.036502463 0.0014 0.0037644739 0.0007368748 0.0337570047 0.0078221753 0.0039807234 0.0022341533 0.0003342918 0.0258256508 0 0.0031118726 0.0059886212 0.0390237536 0.0007556355 0.0096511373 0.0007989301 0.0042099735 +C>A CCG C[C>A]G 0.0008928404 6.77046E-006 0.0019633898 0.0088 0.0028006273 0.0091 0 0.0011596243 0 0.0007 0.001 0.0028 0.0002441665 0.0009 0.0015 0.0022 0.0002974628 0.0171784025 0.0018 0.0124825875 0.0027 0.0009001633 0.0001639537 0.0224289858 0.0012769767 0.000811742 0.0002663122 0.000053652 0.0144961833 0.0022624 0.0031056722 0.0027351313 0.0444175322 0.000426758 0.0104292165 0.0004936949 0.001053447 +C>A CCT C[C>A]T 0.0071865816 0.0004163329 0.0147228611 0.0432 0.0110134658 0.0571 0.0013 0.028791173 0.0091 0.016 0.0014 0.0071 0.0012567682 0.1257 0.0228 0.0084 3.1479429E-005 0.0376769589 0.0096 0.1034012262 0.0056 0.0044398462 0.0007227318 0.0200865154 0.0125636547 0.0190384313 0.00310057 0.0001866719 0.0403550741 0 0.0069708534 0.0135089174 0.0262144919 0.0012449334 0.0241632334 0.0004829446 0.0011918687 +C>A GCA G[C>A]A 0.008232604 0.0003520134 0.0096965397 0.0376 0.011892169 0.0024 0.0003 0.0236823289 0.0118 0.0014 0.0004 0.0062 0.0001321096 0.0018 0.0024 0.0096 0.0065354049 0.1287241581 0.0032 0.0011161238 0.0001 0.0012983702 0.0003499075 0.0546764487 0.0134652951 0.0013753118 0.0107558719 0.0021366291 0.0780466101 0.008853 0.0038823793 0.0123398664 0.0263977944 0.0008119624 0.0094122013 0.0006917252 0.004280167 +C>A GCC G[C>A]C 0.0057580214 0.0001338169 0.0108433411 0.0399 0.0092478575 0.0058 0.0001 0.0158218964 0.0092 0.0022 0.001 0.0056 0.000754244 0.0114 0.0099 0.0094 0.001293804 0.0160928787 0.0031 0.0032714286 0.0038 0.0018096222 0.0005683378 0.109945989 0.0064682981 0.0019616391 0.0124423351 0.0004292084 0.0734609147 0.0093449 0.0070583387 0.0107953358 0.031326093 0.002913003 0.0031021377 0.0010116809 0.003792303 +C>A GCG G[C>A]G 0.0006163352 0.0001784417 0.0009291405 0.0227 0.0028091885 0.0021 0 0.0008509138 0 0.0002 0 0.0015 9.6820775E-005 0.0011 0.0013 0.0036 0.0012836634 0.0092714168 0 0.0037516125 0.0003 0.0003338381 0.0001494178 0.046524869 0.0006581031 1.3229664E-005 0.0016296283 0 0.0173832969 0.0008853 0.0015395666 0.0021848297 0.0263967356 2.28346914246428E-020 0.0025774017 0.000128266 0.0017525461 +C>A GCT G[C>A]T 0.0044590803 0.000122832 0.0122153826 0.0258 0.0103012675 0.0087 0.0001 0.0210612358 0.0085 0.0088 0.0006 0.0027 0.0005511037 0.0736 0.0309 0.0063 0.0031037667 0.0720170701 0.0072 0.0129371945 0.0023 0.0005191482 0 0.0504287095 0.0104730803 0.0019349963 0.0074123552 0.0013185073 0.0596024721 0.0081645 0.0046277367 0.0141566067 0.0151523048 0.0012329031 0.0074480381 0.0009433454 0.0025903332 +C>A TCA T[C>A]A 0.0122500637 0.0151274275 0.0116532249 0.033 0.0147740162 0.0017 0.001 0.027032383 0.0222 0.0374 0.0009 0.0066 0.0481660479 0.0005 0.0057 0.0122 0.0018245583 0.0670806435 0.0051 0.0006882997 0.0001 0.0040516346 0.00207129 0.0314512632 0.0069381466 0.0026800624 0.0070792845 0.0007759028 0.0268944065 0 0.0087885822 0.0073157468 0.0118931991 0.0020899667 0.0100747618 1.06168434038267E-020 0.0011099646 +C>A TCC T[C>A]C 0.0111622293 0.0065324925 0.016606775 0.0538 0.012043465 0.0029 0.002 0.0180897733 0.0043 0.0103 0.0025 0.0099 0.0173295571 0.0166 0.0062 0.0145 0.0012865183 0.0418690097 0.0063 0.0040582291 0.0005 0.0027397709 0.0006964102 0.0625382937 0.0102466074 0.0020316439 0.0062688006 0.0008292925 0.031608137 0 0.0045906893 0.0055555952 0.0228092194 0.0029764847 0.0110724052 0.0011826955 0.0028809145 +C>A TCG T[C>A]G 0.0022754957 0.0016564554 0.0013572394 0.0104 0.0039023624 0.0011 0.0002 0.0016948752 0 0.0031 0.0001 0.0019 0.0022931573 0 0.0025 0.004 0.002172942 0.0151623793 0.0018 0.0010011022 0 0.0005131511 9.9393633E-005 0.0128025907 0 0.0002650717 0.0014464034 0 0.0125004682 0.0016722 0.0007774908 3.70860800590008E-020 0.0151191495 2.28346914246428E-020 0.0080051329 0.000084525 1.63618104265282E-020 +C>A TCT T[C>A]T 0.0152591025 0.0123946107 0.016328076 0.037 0.0182433957 0.0058 0.0013 0.0381413309 0.0322 0.3083 0.0004 0.0049 0.0186345815 0.0516 0.0145 0.0157 0.0050123164 0.1178778467 0.0087 0.0122291045 0.0004 0.0036056509 0.0002074302 0.0302976796 0.0246257872 0.0030171875 0.0098062778 0.0019980737 0.0412071764 0 0.0056468497 0.0041456849 0.016509629 0.0003531941 0.0142205963 0.0004051506 0.0027466457 +C>G ACA A[C>G]A 0.0018010684 0.000263481 0.0240026152 0.0097 0.0116710217 0.0013 0 0.0083568448 0.0048 0.0005 0.0007 0.0031 0.0037751653 0.0001 0.0011 0.0048 0.0016617042 0.0015168876 0.0058 0.0006970411 0.0005 0.000527644 0 0.0119930388 0.0080325676 0.0012728813 0.0013241632 0.000255195 0.0093019711 0 0.0039109532 0.0052086941 0.0112040012 0.0008072133 0.0032995837 0.0011280933 0.0051661719 +C>G ACC A[C>G]C 0.0025809085 0.000269866 0.0121603037 0.0054 0.0072920886 0.0012 0 0.0043063803 0.0023 0.0003 0.0003 0.0015 0.0009208248 0 0.0001 0.0024 0.0016268984 0.0024987845 0.0019 0.00205931 0.0008 0 0 0.0084251198 0.0016359704 0.0015281949 0.0017710841 0.000268899 0.0034790489 0 0.0038915791 0.0021914116 0.004675425 2.28346914246428E-020 0.0017490163 0.0001014437 1.63618104265282E-020 +C>G ACG A[C>G]G 0.000592548 0.0002192339 0.0052754195 0.0031 0.0023038392 0 0 0.0005844153 0 0 0 0 1.9890489E-005 0 0.0006 0 2.5801897E-005 0.002614509 0 0.000012735 0 0 0 0 0 0.0003072463 0 0 0.0001544335 0.00482 0.0015371874 3.70860800590008E-020 0.0113226789 2.28346914246428E-020 0.001844425 0.0001180292 0.0007772772 +C>G ACT A[C>G]T 0.0029639863 0.0006109735 0.0232776563 0.0054 0.0116962457 0.0018 0.0001 0.0086349069 0.0038 0.0002 0.0009 0.0025 0.0038606325 0.0001 0.001 0.0073 0.0013285076 0.0039830112 0.0072 0.0008485871 0.0018 0.0002994547 0 0.0038813832 0.0034284497 0.0024982518 0.0013227198 0.000307698 0.0039767899 0 0.0052747825 0.0105488189 0.0073894579 2.28346914246428E-020 0.0016659161 0.0002700269 0.0020739384 +C>G CCA C[C>G]A 0.0012849834 2.7772077E-005 0.016832572 0.0105 0.0075375232 0 0.0001 0.0066190772 0.0018 0 0 0.0019 0.0053336514 0 0.0009 0.004 0.0019249788 0.0004584638 0.0002 1.331626E-005 0.0001 0.0005820177 0.0001990492 0.0134768216 0.0072007904 0.0012791061 0.0047306494 0.0001033661 0.0026188632 0 0.0031466824 0.0022969107 0.0094396006 0.001675995 0.0044769459 0.0003355716 0.0008847538 +C>G CCC C[C>G]C 0.0007021348 0.0002796439 0.0135314415 0.0097 0.0076332267 0 0.0004 0.0060777029 0.002 0 0.0002 0.0019 0.0009123035 0 0.0003 0.005 0.0007093678 0.0036542283 0.0028 0.0005481447 0 0.0008252996 0.000283776 0.0161056877 0.0045984731 0.0012149773 0.0012616448 0.0001443108 0.0011115123 0 0.0023630851 0.0028433597 0.0102951282 0.0008310079 0.0027673163 0.000052449 0.0003142141 +C>G CCG C[C>G]G 0.0005062896 1.9161576E-005 0.0041764575 0.0063 0.0026137604 0 0.0006 0.0006560334 0 0 0.0008 0 0.0002854673 0 0.0004 0.0028 3.517869E-006 0.0054057742 0.0002 0 0 0.0003821146 0 0.000797472 0.0008237093 0.0002078326 0.0003608566 0 0.001520047 0.0032461 0.0015435318 0.0054040236 0.0106255283 0.0008310033 0.0018344572 0.000004761 0.0013964056 +C>G CCT C[C>G]T 0.0013815427 0.0003127816 0.0240463904 0.0094 0.0094170979 0.0002 0.0003 0.007805027 0.0039 0 0.0002 0.0019 0.0063830976 0 0.0017 0.008 0.0009537763 0.0055196048 0.0008 0.0001207306 0.0003 0.0017606459 0.0001957753 0.0103886659 0.0001963603 0.0022970262 0.0002680262 0.0002909995 0.0001397507 0 0.00319971 3.70860800590008E-020 0.0068522711 0.0004239346 0.0056157952 0.0001926151 0.0005915023 +C>G GCA G[C>G]A 0.0006021227 4.4838514E-005 0.0119168446 0.007 0.0055594231 0 0 0.0037245679 0.0011 0 0 0.0012 0.0013494196 0.0002 0.0022 0.0031 0.0012963242 0.0009238797 0.002 0.0013397693 0.0004 0 0 0.0049450607 0.0041696555 0.0013206075 0.0014181664 8.1591411E-005 0.0002657599 0.0073775 0.00153378 0.0041577528 0.0048126831 2.28346914246428E-020 0.0030944242 0.0003675084 0.001523035 +C>G GCC G[C>G]C 0.0023933522 1.4520103E-005 0.0098236534 0.0091 0.0053888012 0.003 0.0004 0.003046597 0.0029 0.0002 0.0002 0.0011 0.0007888077 0.0001 0.0005 0.0032 0.0002607609 0.0006486479 0 0.0018111515 0.0042 0 0.0001375011 0.0093698758 0.0023928049 0.0018455011 0.0013467168 0.000105219 0.0009450129 0.0065906 0.0608517207 0.0190915784 0.0509667244 0.0047167891 0.0031230002 1.06168434038267E-020 0.0020402151 +C>G GCG G[C>G]G 2.48534E-007 4.0665889E-005 0.0016710543 0.0062 0.0011005896 0 0 0.0003212128 0 0 0 0 8.1791214E-005 0 0.0006 0 4.377552E-006 0.00054284 0 6.37538E-007 0 0.0002146959 0 0.0056257265 0.0004181939 0.0002050608 0 0 0 0.0015739 3.27595444415171E-020 0.0050892581 0.0129626353 0.0012642272 0.001539434 0.0001210511 0.000894833 +C>G GCT G[C>G]T 0.0008900807 0.0002684295 0.0179143343 0.006 0.0060412478 0.0017 0 0.0057756636 0.0044 0.0004 0 0.0009 0.0026801232 0.0003 0.0018 0.0029 0.0018203928 0.0013767249 0 0.0012382642 0.0004 0.0005384388 0 0.0030557701 0.0019940122 0.0012255329 0.004560686 0.0001596794 0.0047967447 0 0.0086309368 0.022922438 0.011972958 0.0024557172 0.0039954749 0.0005706812 0.000676421 +C>G TCA T[C>G]A 0.0018748532 0.0372418531 0.0160414054 0.0032 0.002681057 0 0.0002 0.0041178788 0.0033 0 0.0001 0.0024 0.2802349465 0 0.0009 0.005 0.0003926847 0.0018029691 0.0005 2.4298469E-005 0.0002 0.0002254906 0.0002306089 0.0102208574 0.0097987246 0.0042018968 0.0028704337 0.0005213704 0.0008204449 0 0.0062124849 0.0015481065 0.0098767034 0.0003657106 0.0027951387 0.0001697674 0.0004808179 +C>G TCC T[C>G]C 0.0020674188 1.9413411E-005 0.0201499204 0.0105 0.0079240483 0.0002 0.001 0.0037996496 0.0025 0 0.0011 0.0027 0.0638852866 0 0.0026 0.0064 0.0006556024 0.0078630068 0.0011 0.0001519986 0.0003 0.000628695 0.000165787 0.0075783653 0.0032665072 0.0028077615 0.0031079676 0.0006673259 0.0004441193 0 0.0046382358 0.0015499829 0.0104195164 2.28346914246428E-020 0.0038186331 0.0009660426 0.0020253166 +C>G TCG T[C>G]G 0.000304897 0.0016254655 0.0025279109 0.0031 0.0013190756 0 0.0003 0.000025653 0 0 0.0003 0 0.009528486 0 0 0 1.3641541E-005 0.0015132233 0 0 0 0.000395808 0 0.0015927142 0.0020574368 6.197E-009 1.2810409E-005 0 0.0001432972 0.0019673 0.0023939233 0.0002293998 0.0040902531 2.28346914246428E-020 0.0026731185 8.65095809094198E-005 0.0006634679 +C>G TCT T[C>G]T 0.0031515745 0.0668798997 0.0326736408 0.005 0.0066445957 0.0001 0.0007 0.0062475537 0.0049 0.0001 0.0008 0.0015 0.3302254817 0.0001 0.0015 0.0169 0.0028523804 0.0035671021 0.0105 0.00068306 0.0003 0.0002573751 0.0004389558 0.0061007272 0.0164009169 0.008019383 0.0021305875 0.0012457795 0.001369869 0 0.0109379855 0.0079398101 0.0198199846 0.0007988588 0.0031000891 0.0004375033 0.00213264 +C>T ACA A[C>T]A 0.0295145327 0.0074415568 0.0178721707 0.012 0.0218391876 0.0312 0 0.0180666872 0.0093 0 0.0225 0.0121 0.0014801808 0.0293 0.0117 0.0135 0.0093504884 0.0038256239 0.0221 0.0328580473 0.0051 0.0031133897 0.0197671544 0.0063155181 0.0209876181 0.005907232 0.0137232858 0.0054337925 0.0051972213 0.065119 0.0012054247 0.0320885261 0.0098060082 0.0225701805 0.0023906012 0.031397907 0.0109990991 +C>T ACC A[C>T]C 0.014322747 0.0027263124 0.0088960343 0.0075 0.0127561056 0.0163 0.0197 0.005650015 0.0056 0.0032 0.1099 0.0054 4.0508707E-005 0.0321 0.0169 0.0076 0.004224289 0.0024652143 0.0203 0.0221960469 0.0062 0.0015248603 0.0818805799 0.0038443269 0.0131412837 0.0106264578 0.005424306 0.0018154155 0.00897647 0.054397 0.0020840175 0.0247589098 0.000014969 0.1193404879 0.0011790037 0.1281792372 1.63618104265282E-020 +C>T ACG A[C>T]G 0.1716469313 0.0033220833 0.0035727084 0.0028 0.0167601771 0.0908 0.0001 0.0192651055 0.0125 0.0126 0.0072 0.0019 0.0003165947 0.0496 0.0309 0.0035 0.0092292133 0.0084639569 0.0368 0.0345720147 0.0256 0.0036256412 0.0092487151 0.0031106644 0.0196598943 0.0199303232 0.0067064295 0.0054320393 0.0316389964 0.0204604 0.0054138542 0.0094650035 0.0135229545 0.0067748274 0.0006406472 0.0049427727 0.0041432056 +C>T ACT A[C>T]T 0.0126237632 0.0033265284 0.0147976122 0.0059 0.0164779547 0.0149 0.0043 0.0208059675 0.0076 0.0047 0.0639 0.0067 0 0.0277 0.0066 0.0101 0.0057359612 0.0056057399 0.0266 0.0188195596 0.003 0 0.0332096522 0.0034204187 0.0057285193 0.0113345306 0.004475614 0.0016292132 0.0047696666 0.0219359 3.27595444415171E-020 0.039006119 0.0014857753 0.071059016 0.001827398 0.105189432 0.0084673356 +C>T CCA C[C>T]A 0.020896447 0.0150195069 0.0143950595 0.021 0.0227692094 0.0085 0.0754 0.00486581 0.0098 0.0012 0.031 0.0187 0.0036472785 0.006 0.0051 0.021 0.0212652059 0.0097675115 0.0438 0.0111451853 0.0034 0.0077313495 0.0605726278 0.0060354474 0.0143339947 0.0065944449 0.0174384848 0.0043915326 0.0091264718 0.0694472 0.0155033821 0.0149734308 0.0134135166 0.0208371809 0.0031630949 0.0221027852 0.0251652379 +C>T CCC C[C>T]C 0.0185017048 0.0035169181 0.0085447812 0.0144 0.0175094763 0.0099 0.1007 0.0039801504 0.0069 0.0024 0.1518 0.0094 0.0010042293 0.0167 0.0088 0.0098 0.0038472353 0.0056548285 0.0753 0.0181527469 0.0091 0.0071108505 0.1863756341 0 0.0059366437 0.006510632 0.0071448702 0.002647661 0.007067603 0.0638403 0.013021492 0.0277530953 0.0035533335 0.1090353647 0.0023361199 0.1200792204 0.0098240362 +C>T CCG C[C>T]G 0.0955772173 0.0049792757 0.0035184658 0.0076 0.0128622376 0.0901 0.0208 0.0083386392 0.0076 0.0109 0.0135 0.0046 0.0001292021 0.0293 0.0155 0.0016 0.0131761123 0.016183223 0.0238 0.0443849425 0.0318 0.005502031 0.0151490826 0.0029244191 0.0115593916 0.0119049353 0.0075035617 0.0022845636 0.0198751804 0.0173126 0.0093878242 0.0106000807 0.0086266994 0.0033373046 0.0008153359 0.0054361338 0.0109032677 +C>T CCT C[C>T]T 0.0171133076 0.0089565528 0.0160755457 0.0201 0.0204295134 0.0087 0.0788 0.0188436274 0.0097 0.0043 0.0816 0.0205 0.00061177 0.0186 0.0096 0.0211 0.0096480253 0.0051533186 0.1159 0.0138471362 0.004 0.0041697772 0.156015397 0.0039712016 0.0136325969 0.0062385563 0.0071480277 0.0024239843 0.0016340587 0.0342318 0.0037452885 0.0170644264 0.0034364665 0.0750337534 0.0023529602 0.0989779779 0.0459700918 +C>T GCA G[C>T]A 0.0249438142 0.0063908079 0.0161272733 0.0087 0.0200382586 0.0653 0 0.0022612627 0.0062 0 0.0261 0.0124 0.0029341376 0.0557 0.0476 0.0125 0.0020687547 0.0027030687 0.0374 0.056793948 0.0163 0.0019153709 0.053282059 0.0236790513 0.010038112 0.009606515 0.0142153137 0.0033842409 0.011638793 0.0485934 0.0048229646 0.0892436272 0.0043067164 0.0306663268 0.0013973066 0.0214764258 0.0106870051 +C>T GCC G[C>T]C 0.027161494 0.0019958168 0.0082086324 0.008 0.0180223122 0.0773 0.021 0.0016166492 0.0069 0.0134 0.0975 0.0092 0.0025151711 0.0618 0.1345 0.0092 0.0003254834 0.0041993075 0.0614 0.0544298573 0.0392 0.0032291335 0.1629183437 0.0159192018 0.0069538752 0.0195074267 0.0201436462 0.001687414 0.0037817517 0.0494787 0.0037100764 0.0856648665 0.0003026637 0.105842878 1.64761887388717E-005 0.0782012229 0.0060785799 +C>T GCG G[C>T]G 0.1035707623 0.000303021 0.0012129229 0.0023 0.0131938176 0.1339 0.0002 0.0116067116 0.0088 0.027 0.009 0.0023 0.0032052646 0.0978 0.1829 0.0009 0.0075111014 0.0118973608 0.0278 0.0045926886 0.0019 0.0033005989 0.0130464947 0.0126480776 0.010468363 0.0225027174 0.0093684685 0.002189309 0.019684388 0.0157387 0.0091644502 0.0308714868 0.0101967765 0.0097694965 0.0014993181 0.0044460527 0.0093497401 +C>T GCT G[C>T]T 0.0176898544 0.0032658182 0.0106116492 0.0082 0.0195029153 0.0524 0.0161 0.006284929 0.0101 0.0152 0.0522 0.0115 0.0016877305 0.0555 0.08 0.0116 0.0009256972 0.0019133809 0.0917 0.0495808638 0.0166 0.0011140596 0.1075903998 0.0181297784 0.0098238207 0.0173074722 0.007589626 0.0010439936 0.0057613368 0.0188865 0.0016456849 0.1762001422 0.000252515 0.0705253792 0.0007327716 0.0704268438 0.0252314948 +C>T TCA T[C>T]A 0.0144920996 0.4199413996 0.0088802091 0.0035 0.0109975603 0.0074 0.1202 0.0071806685 0.005 0.0037 0.0302 0.0138 0.1138420932 0.0092 0.0112 0.0172 0.0161007846 0.0149233917 0.0218 0.0107103221 0.0064 0.0020167217 0.0145586137 0.0265718943 0.0110775208 0.0113032888 0.0187577765 0.0076222577 0.0120765831 0.0849892 0.00612291 0.016765482 0.0101245636 0.0216295113 0.0004213732 0.0198210105 0.0106059003 +C>T TCC T[C>T]C 0.0176807754 0.0819724961 0.0135295728 0.007 0.0206449648 0.0067 0.2887 0.0040610329 0.0084 0.0211 0.1589 0.0095 0.015024839 0.0283 0.0156 0.0131 0.0167799841 0.0099627443 0.033 0.0081755098 0.0086 0.0019908342 0.0435104469 0.0120556911 0.0064487875 0.010807527 0.0079891844 0.0051166192 0 0.090301 0.0108921843 0.0179803954 0.003814104 0.1327623933 0.0020981333 0.1253180687 0.0045197968 +C>T TCG T[C>T]G 0.0760022217 0.0477201864 0.0017054089 0.0011 0.0075344896 0.0391 0.0992 0.0055351215 0.0047 0.2141 0.008 0.001 0.006102098 0.0094 0.0104 0.0036 0.0162720956 0.0115497151 0.009 0.0231638992 0.0126 0.0014984731 0.0027526405 0.0053633597 0.0140834162 0.0103643293 0.004609131 0.0019180281 0.0158301968 0.0151485 0.0014706199 0.0150859914 0.0140381297 0.0050845027 0.000657358 0.0043935397 0.006429352 +C>T TCT T[C>T]T 0.013761704 0.2286749183 0.0103044169 0.0077 0.0117874618 0.0047 0.0844 0.0122090705 0.0096 0.0392 0.0954 0.009 0.0281406612 0.0229 0.0076 0.0193 0.0198274176 0.005398014 0.0267 0.0095400872 0.0064 0.0011822265 0.0243287852 0.0055324992 0.0124185859 0.0072491454 0.0118809325 0.0061931586 0.0134621373 0.045544 0.0038110945 0.0225109222 0.0040578949 0.0981830992 0.0023085876 0.1184227677 0.0281680921 +T>A ATA A[T>A]A 0.0040215203 1.32377E-007 0.0084285636 0.0048 0.0089029043 0.0006 0.001 0.0133650828 0.0121 0 0.0002 0.0058 0.0012436183 0 0.0021 0.0081 0.0006130025 0.0030372108 0.0011 0.0005744014 0.0083 0.0496192297 0 0.0011667471 0.0204305271 0.0044593399 0.143076389 0.0009640309 0 0.0075743 0.0213988628 0.0016153942 0.0036242193 2.28346914246428E-020 0.0044936789 0.0004435178 0.0078378864 +T>A ATC A[T>A]C 0.0023711442 0.0001130696 0.0073730967 0.0039 0.0073992025 0.0033 0.0008 0.0124312021 0.0042 0.0002 0.0001 0.0065 0.0010600019 0.0008 0.009 0.0073 0.0018785875 0.0008111672 0.0053 0.0019714621 0.0292 0.0116667405 0 1.5173057E-005 0.0088925607 0.0128222429 0.0014640854 0.0033656678 0.0030495957 0.003738 0.0046842304 0.0039533946 0.001510433 0.0012607026 0.008807992 0.0004945331 0.0054454405 +T>A ATG A[T>A]G 0.00281091 0.0005329294 0.0073573 0.01 0.0115080515 0 0.0009 0.0140366571 0.0068 0 0.0007 0.0046 0.0001025544 0 0.0009 0.008 0.0010873497 0.0045032071 0.0045 0.0001905866 0.0027 0.0679154542 0.0002374185 0.0063324556 0.0062419485 0.0011723443 0.0012262809 0.0017857537 0.003909982 0.0065906 0.0583714179 0.0049727586 0.0085456931 3.92791895501103E-020 0.0474446131 1.06168434038267E-020 0.0272805461 +T>A ATT A[T>A]T 0.0083609093 0.000149111 0.008753939 0.003 0.0111936232 0.0053 0.0035 0.0241099166 0.0185 0.0012 0.0003 0.006 0.0009718121 0.0009 0.0079 0.0084 0.0020454937 0.0027365232 0.0033 0.0074211035 0.0043 0.0145999176 0 4.967216E-006 0.0148508776 0.0039931375 0.002535198 0.0056530891 0.0051055274 0.0093447 0.0070547539 0.0025332903 0.0049596807 0.0003670923 0.0097010208 0.000250913 0.0076822653 +T>A CTA C[T>A]A 0.0011825874 0.000154599 0.0075713203 0.0075 0.0050431635 0.0001 0 0.0120242175 0.0055 0 0.0004 0.0017 0.000285159 0 0.0016 0.0054 3.0079241E-005 0.0004123464 0.0043 4.5042364E-005 0 0.0868985455 0.0005945285 0.0027666348 0.0262963231 0.0035614227 0.3306010175 0.00256658 0.0017654475 0.0053118 0.0483959361 3.70860800590008E-020 2.80409853263637E-020 0.0004214101 0.0030069836 8.83773649853599E-005 0.016911196 +T>A CTC C[T>A]C 0.0019031669 0.000464019 0.0127254635 0.0111 0.0062088437 0.0026 0.0014 0.0178810924 0.0049 0.0001 0.0011 0.0086 0.0002222873 0.0034 0.0043 0.0128 0.0102237477 0.0024914113 0.0053 0.0043890556 0.0037 0.0537068468 0 0.0026944625 0.0157998831 0.003901611 0.0028135988 0.0196108974 0.0003833591 0.0067873 0.0529238918 0.0055241267 0.0121689451 0.0004418274 0.0464989794 0.0002839599 0.0201908902 +T>A CTG C[T>A]G 0.0014879606 0.0002304098 0.0115085619 0.0342 0.010507569 0.0008 0.0007 0.0163567745 0.0051 0.0003 0.0006 0.0031 0.0002869518 0.0002 0.0027 0.013 0.0044670362 0.0055230457 0.0021 0.0011278358 0.0025 0.2132208666 0.0001731204 0.0069111647 0.0628606064 0.0023903042 0.0043968571 0.0088336 0.0035568452 0.0082628 0.1374715155 0.0042244367 0.0171153481 0.0023322216 0.1759940642 0.0004900921 0.0652277252 +T>A CTT C[T>A]T 0.0021793444 0.0005748856 0.0164561777 0.0115 0.0097846407 0.0011 0.0018 0.0262478019 0.0069 0.0009 0.0004 0.0054 8.00446E-007 0.002 0.0007 0.0096 0.0312448834 0.0033137133 0.0022 0.0023855413 0.001 0.0618275075 0.0004578131 0.0029152002 0.0366223511 0.0016359227 0.0054308916 0.0109426098 0.0022327555 0 0.0421848137 0.0095318815 0.0120375101 0.0032148689 0.0636503124 1.06168434038267E-020 0.0262779434 +T>A GTA G[T>A]A 0.0006892894 0.0001149942 0.0044347826 0.0069 0.0067403877 0 0 0.0081391786 0.003 0 0.0003 0.0015 0.0001379604 0 0 0.003 8.545689E-006 0.0018754341 0.0026 0.0001631298 0 0.0537091457 0 0.0022251273 0.0362178008 0.0022428865 0.109851872 0.0005514608 0.0029300981 0.003738 0.0446039243 3.70860800590008E-020 0.0011458553 2.28346914246428E-020 0.0242716316 0.0003044765 0.0042013058 +T>A GTC G[T>A]C 0.0005524095 0.0002938621 0.0056154324 0.0052 0.0040215965 0.0028 0 0.0079100803 0.0029 0.0001 0.0003 0.0039 0.0002528674 0.0025 0.0038 0.004 0.002573467 0.0015103098 0 0.0037991795 0.0142 0.0094893967 0.0001832038 0.0048531492 0.0058471096 0.0052072871 2.3455678E-005 0.0031639876 0 0.0033445 0.0125235888 0.0030277907 0.0012285467 0.0008083668 0.0179461702 0.0002367232 0.0016197032 +T>A GTG G[T>A]G 0.0012002288 8.8721344E-005 0.0080701365 0.0133 0.0068143523 0.0006 0.0006 0.0090572631 0.0028 0 0.0004 0.0019 0.0001535175 0 0.0026 0.0051 0.0035388226 0.0015053688 0.0016 0.0008283337 0.0031 0.0502939024 0 0.0001957586 0.0382411793 0.0013581218 0.0015659372 0.002152847 0.0005336324 0.0050167 0.0460502984 0.0010906538 0.0077826056 0.0019375384 0.103954526 0.0003980643 0.0218805741 +T>A GTT G[T>A]T 0.0021071368 0.0002157555 0.0086791217 0.0045 0.0051010329 0.0021 0.001 0.0178122386 0.0036 0.0004 0.0001 0.0031 0.0001227456 0.0009 0.0043 0.0033 0.00387901 0.0036110252 0.0052 0.0019007466 0.0041 0.0106014572 0 0 0.0201679544 0.0025131129 0 0.0020077332 0 0.0063939 0.007042014 0.0029648102 0.0046125727 0.0021050728 0.0298636223 0.0002916778 0.0067356063 +T>A TTA T[T>A]A 0.0056001554 8.0752486E-005 0.0071326814 0.0045 0.0092056373 0.0002 0.001 0.0151399962 0.0215 0 0.0003 0.0057 0.0004032613 0 0.0008 0.0085 0.0006988123 0.004663278 0.0039 0.000924548 0.0027 0.0408105028 0 0 0.021830329 0.0006281453 0.0528138875 0.0002032376 0.0011912074 0.0076726 0.0184166439 3.70860800590008E-020 0.002312234 2.28346914246428E-020 0.0040023292 6.85246736359736E-005 0.0119031697 +T>A TTC T[T>A]C 0.0019990793 4.802898E-006 0.0091027978 0.0046 0.0068353442 0.0008 0.0015 0.0120935546 0.0027 0.0008 0 0.0132 0.0007718133 0.0016 0.0019 0.0087 0.0025793586 0.0025781555 0.0048 0.0007082068 0.0045 0.0255703958 0 0.0079941292 0.0034056867 0.0050737539 4.7091785E-005 0.0101809649 0.001682664 0.0064922 0.0160946246 0.0018285335 0.0003268915 0.0012342766 0.0149322709 8.55752603112063E-009 0.0107582495 +T>A TTG T[T>A]G 0.0010900657 0.000066605 0.006565863 0.0082 0.0071442088 0 0.001 0.0083625466 0.014 0 0 0.0037 0.0002451942 0 0.0006 0.0063 2.1133639E-005 0.0020167384 0.0052 9.7003127E-005 0 0.0698452181 0.0002315256 0.0112021436 0.0101915204 2.0138391E-005 0 0.0032504272 0.002438756 0.0036396 0.040365198 0.0032796029 0.0053251107 0.0007275037 0.0496236886 1.06168434038267E-020 0.0207078591 +T>A TTT T[T>A]T 0.0039810228 0.0002763159 0.0147121354 0.0045 0.0102408504 0.0007 0.005 0.0276532963 0.0139 0.0028 0.0008 0.0094 0.000160346 0.0012 0.0003 0.008 0.0038831306 0.0028186794 0.0085 0.0023134891 0.0008 0.0235790618 0 0.0002705788 0.0145275393 0.0012355385 0.0019297708 0.0164928123 0 0 0.0069546395 0.0010941496 0.0014059298 2.28346914246428E-020 0.0123523838 1.06168434038267E-020 0.0111784782 +T>C ATA A[T>C]A 0.013915773 0.0013035096 0.0130357094 0.0084 0.0353667351 0.0075 0.0005 0.0162065101 0.0252 0.0031 0.0006 0.0466 0.0005494542 0.0026 0.0115 0.0717 0.002697314 0.0029330536 0.0145 0.016395063 0.0265 0.0168399309 0.0010684488 0.0047260091 0.0206632828 0.0550286521 0.0050473011 0.0040927469 0.0101191812 0 0.0007369268 0.0018982472 0.0032086778 0.0021449978 0.0012492827 0.0008360974 0.0167611068 +T>C ATC A[T>C]C 0.0062749606 0.0004255767 0.0091862897 0.002 0.0137711021 0.0056 0.0001 0.0077878028 0.0105 0.0052 0.0015 0.0317 0.0001455067 0.0046 0.0073 0.0171 0.0080781501 0.0015132848 0.0048 0.0192517936 0.0165 0.0011082624 0.0002215732 0.0006279493 0.0095024784 0.0275946042 0.0018456912 0.0078807292 0.0063496827 0.0087547 0.0023157171 0.0082384411 0.0047295938 0.0016959289 0.0037492625 0.0014204736 0.0368452578 +T>C ATG A[T>C]G 0.0101376362 0.000575473 0.0117169201 0.0081 0.0284490517 0.0217 0.0007 0.0098525836 0.0176 0.0026 0.0008 0.0487 0.000279178 0.0035 0.0073 0.0348 0.0044328707 0.003329669 0.0135 0.054784918 0.0224 0.0049136164 0.0004988015 0.0027237586 0.0199114925 0.0517910441 0.0056888139 0.0055208336 0.0146596103 0.0090498 0.0117071286 0.0155936441 0.0199843865 0.0033499277 0.0082514297 0.0004135217 0.0267834634 +T>C ATT A[T>C]T 0.0092563164 0.0014881641 0.0169788708 0.0036 0.0273029742 0.0023 0.0011 0.0218294638 0.0247 0.004 0.0003 0.025 0.0002674614 0.0025 0.0063 0.0497 0.0031403702 0.0054913178 0.016 0.0073412699 0.0189 0.0026305239 0.0003132405 0.0071223685 0.0144883903 0.0390722444 0.0025927546 0.003232484 0.0078924134 0 0.0032016902 0.0009747108 0.0057597756 0.0016824476 0.0037991583 1.52941700565386E-005 0.0221085555 +T>C CTA C[T>C]A 0.0041766749 0.0005466192 0.0078950126 0.0052 0.0142386298 0.0062 0.001 0.0051738424 0.0154 0.0005 0.0001 0.0312 4.2751466E-005 0.0006 0.0032 0.0146 0.0074269996 0.0001921693 0.0066 0.0148676965 0.0219 0.0040273463 0 0.0018488765 0.0090280149 0.0378893777 0.0048990792 0.0207380034 0 0 3.27595444415171E-020 3.70860800590008E-020 0.0037334463 0.0012694857 0.0030605132 0.0002793274 0.0094075061 +T>C CTC C[T>C]C 0.0052525933 0.0003923326 0.0144311704 0.0026 0.0124895004 0.004 0.0008 0.0109368938 0.0118 0.0019 0.0004 0.0385 4.3307542E-005 0.0053 0.005 0.0194 0.0396570012 0.0030501926 0.007 0.018356161 0.01 0.0013524439 0 0.0044536899 0.0107716324 0.021740735 0.0057244485 0.0432837972 0.0027749537 0 0.0079452901 3.70860800590008E-020 0.0108649219 0.0037894225 0.0097182676 0.0009258279 0.0446116027 +T>C CTG C[T>C]G 0.0070132253 0.0003620245 0.0084229721 0.01 0.0187416312 0.027 0.001 0.0056577736 0.0154 0.0015 0.0001 0.0415 5.4272534E-005 0.0016 0.0128 0.019 0.0286096963 0.0025964642 0.004 0.0741505626 0.0211 0.0027496661 0.0003207049 0 0.0133506613 0.0472401033 0.005661479 0.0370882617 0.0069024147 0 0.0053848162 0.0065013981 0.0174152084 0.0029716741 0.0100054171 0.0008548023 0.01561524 +T>C CTT C[T>C]T 0.0067138131 0.0005609001 0.0119324305 0.0054 0.0190540829 0.0033 0.0045 0.0111203893 0.0275 0.002 0.0009 0.0324 7.63944E-007 0.0027 0.0035 0.0263 0.1018696577 0.0013100287 0.0053 0.0110011183 0.0204 0.0023633535 0 0.001597389 0.00896103 0.0207406214 0.0039005891 0.005052716 0.0030414249 0 0.0126209242 0.0081108597 0.017359194 0.0016698115 0.0079776445 0.0003108439 0.0303223841 +T>C GTA G[T>C]A 0.0112478351 4.673852E-006 0.0068500556 0.0061 0.0162949828 0.0122 0.0002 0.0057207785 0.0091 0.0064 0.001 0.0573 0.0010540812 0.0078 0.0195 0.0161 1.1401335E-005 0.0005291265 0.0039 0.0024693171 0.1426 0.0042174541 0.0002511686 0.0012697498 0.0174898239 0.0980528247 0.0047773804 0.0036550481 0.0070908038 0 0.0047403321 0.0019137689 0.0019750503 0.0016904982 0.0033999956 0.0020780793 0.0238767847 +T>C GTC G[T>C]C 0.0069997243 0.0001860659 0.006260749 0.0016 0.0095745606 0.0059 0.0001 0.0051810515 0.0097 0.0101 0.0016 0.0274 0.0005298997 0.0127 0.0499 0.0099 0.0096577133 0.0022791308 0.003 0.0015656329 0.0665 0 0.0005382185 0.00671034 0.0040456124 0.040226364 0.0019649543 0.0070711753 0.0071113275 0.0065906 0.0095055012 0.0067394905 0.007108284 0.007601967 0.0066302715 0.0028938432 0.0373426928 +T>C GTG G[T>C]G 0.0049775926 0.000000495 0.006098763 0.0042 0.0141039293 0.0115 0.0003 0.0050407075 0.0094 0.0054 0.0019 0.041 0.0006300957 0.0082 0.0154 0.0148 0.0046541291 0.0058710566 0.006 0.027341755 0.0884 0.0014748845 0 0.000277685 0.0134022463 0.044620701 0.0012291677 0.0082322384 0.0056430636 0.0078694 0.0062721008 0.0110147688 0.0095895668 0.001697214 0.0095595352 0.0017103342 0.0446625918 +T>C GTT G[T>C]T 0.0106674061 0.0005785981 0.0075093439 0.0024 0.0156668747 0.0042 0.0081 0.0084882203 0.0126 0.0124 0.0023 0.0405 0.0006761879 0.0086 0.0094 0.0142 0.0081492346 0.0047715657 0.0099 0.0014982648 0.1003 0.0015610427 0.0009957697 0.0042384777 0.0141596937 0.0555280683 0.003747225 0.0004078845 0.0112376743 0.0084596 0.0022664575 0.0082567832 0.0036822191 0.0016897626 0.0039742914 0.0018309055 0.037512717 +T>C TTA T[T>C]A 0.0080736164 0.0001019324 0.0091154951 0.0028 0.017059641 0.0059 0.0023 0.0049010724 0.0156 0.003 0.0002 0.05 0.0007840561 0.0018 0.0068 0.0246 0.0017085867 0.0003023036 0.0052 0.0057342296 0.0389 0.0048036697 0 0.001682291 0.0145150501 0.0287896805 0.0017210153 0.0099295521 0.011498666 0 0.0014804542 3.70860800590008E-020 0.0005155448 0.0004342265 0.0002008934 2.69491298125691E-005 0.0095996027 +T>C TTC T[T>C]C 0.0048573812 0.0004703437 0.0109537909 0.0016 0.0141957091 0.0035 0.0018 0.0060810113 0.0137 0.0097 0.0009 0.0342 0.0001329749 0.0056 0.0099 0.0183 0.0110741521 0.0062607911 0.002 0.0112342547 0.0313 0.0009121575 0.0002306089 0.0023445277 0.0074060835 0.0366394924 0.0034892126 0.0290105632 0.003584215 0.0091481 0.0007815096 0.001861857 0.0043626179 0.0012602376 0.0045334937 0.0024327604 0.0226722212 +T>C TTG T[T>C]G 0.0083254542 0.0001923542 0.0061130332 0.0036 0.0125965017 0.0106 0.0019 0.0017124847 0.0098 0.0065 0.0007 0.032 3.7402404E-005 0.0034 0.0039 0.0165 0.0059320028 0.0015412653 0.0057 0.0237676113 0.0249 0.0017817357 0.0002395138 0.0004812742 0.0048925312 0.0191436943 0.0011528466 0.0156832186 0.0016942967 0.0060004 0.0007662323 3.70860800590008E-020 0.0026293456 0.0012747632 0.0024208246 0.0006974434 0.0094636702 +T>C TTT T[T>C]T 0.0062571056 0.0005853303 0.0107743363 0.0022 0.0173751391 0.0029 0.0024 0.0100034418 0.0309 0.0099 0.0005 0.0371 0.0001797028 0.0026 0.0047 0.0174 0.0072082184 0.0013577971 0.0038 0.0053951863 0.0274 0 0 0.000358148 0.0170147808 0.0230716888 0.001527957 0.0172915636 0.0037997058 0 0.0032239339 0.0005133397 0.0022567107 2.28346914246428E-020 0.0010789385 0.0009168841 0.0203240337 +T>G ATA A[T>G]A 0.0015876364 3.3718411E-005 0.0023513681 0 0.003462152 0 0 0.0042197193 0.0335 0 0 0.0012 0.0003861998 0 0 0.0052 5.3139249E-005 0.0003861382 0.0014 1.765291E-006 0 0.0016519986 0 0 0.0052816797 8.0653426E-005 0.0011363374 0.0063646756 0 0.0053118 0.0032703303 0.0015043531 0.0028023351 0.0003957761 0.0014441538 9.63385814248833E-005 0.0036558173 +T>G ATC A[T>G]C 0.0017840913 2.4844826E-005 0.0014642311 0.0002 0.0022465927 0.0017 0 0.0007936713 0.0051 0.004 0 0.001 0.0001123832 0.002 0.0006 0.0042 0.0064686613 0.0012549821 0 0.0003813879 0.0031 0 0 0.0014639507 0 0.0001631712 0.0009589764 0.0166109056 0 0.0024592 0.0055761328 3.70860800590008E-020 0.0078161802 0.0016649968 0.0016409129 0.0001054276 0.0009645819 +T>G ATG A[T>G]G 0.0013858306 0.0002734541 0.0090537776 0.0015 0.0054902168 0.0007 0.0009 0.0068658004 0.0052 0.0015 0.0001 0.0018 3.6000696E-005 0.0007 0.0012 0.0061 0.003481549 0.0023692161 0.001 0.0006587581 0.0016 0.0010868728 0 0.0008476125 0.0071364216 0.0012550795 6.766061E-005 0.0065928422 0.0029251714 0.0062955 0.0201754566 0.0174806227 0.0270345909 0.0016119211 0.0052592527 8.9297393290661E-005 0.0025491352 +T>G ATT A[T>G]T 0.0031585393 0.0002176949 0.0070309764 0.0002 0.0038212267 0.0029 0 0.0029399223 0.0193 0.0137 0 0.003 0.0001924938 0.0056 0.0029 0.0076 0.0309263752 0.0003386029 0.0017 0.0005321252 0.0018 0 0 0.0010754553 0 0.0018503835 0.0002560277 0.0863928974 0 0.0095416 0.0054223733 0.0017155767 0.0053889069 0.0008560725 0.0008122481 1.4899146840365E-008 0.0001871482 +T>G CTA C[T>G]A 0.0003026912 0.0001137846 0.0019741811 0 0.0020416489 0.0001 0 0.0024240506 0.0216 0.0022 0 0.0013 1.5094208E-005 0 0 0.0002 9.1469787E-005 6.1002548E-005 0 2.3264084E-005 0 0.0011203565 0 0 0 9.539626E-005 0 0.0095898419 0.0011168548 0.0046233 3.27595444415171E-020 3.70860800590008E-020 0.0005262194 0.0004210208 0.0042847979 0.0002891821 0.001843657 +T>G CTC C[T>G]C 0.0020985024 2.2095087E-005 0.0058242955 0.0013 0.0034785021 0.004 0.0008 0.0020962106 0.0064 0.0018 0.0001 0.0049 0.0001476248 0.002 0.0019 0.0082 0.0198142936 0.0020156969 0.0011 0.0084764945 0.0005 0.0010645836 0.0001901443 0.0021854373 0.0028864543 0.0039194551 0.000381245 0.0339132237 0 0.0060004 0.0039803758 0.0025376549 0.0060513622 2.28346914246428E-020 0.0088482202 0.0009775125 0.0090219017 +T>G CTG C[T>G]G 0.0015995485 0.0002282459 0.0104646545 0.0046 0.0071474562 0.005 0.0009 0.0066040463 0.0126 0.0037 0.0011 0.0045 4.59873E-005 0.0005 0.0007 0.0067 0.0134498376 0.0053119673 0.0013 0.0153837761 0.0004 0.0041885681 0 0.0001139097 0.0117694925 0.0054973573 0.0004032572 0.0185164816 0.0021696933 0.0073775 0.0039200627 0.0028967736 0.007564699 0.0003827374 0.0207298099 1.06168434038267E-020 0.003023422 +T>G CTT C[T>G]T 0.0027585376 6.711134E-005 0.0087243873 0.0012 0.0114868115 0.0086 0.0013 0.0048667139 0.0509 0.0182 0.0009 0.0063 0.0004637147 0.0063 0.0045 0.0186 0.2614566141 0.0023416292 0.0019 0.0021853947 0.0032 0.0016294096 0.000210835 0.0025337183 0.0085508075 0.0067887187 0.0014390961 0.118967103 0.0011436633 0.0091481 0.0157841091 0.012870271 0.0262293556 0.0019670653 0.0047092177 0.0002687511 0.003570495 +T>G GTA G[T>G]A 0.000099045 9.5552392E-005 0.004144488 0 0.0016276645 0 0 0.0009745787 0.0072 0 0 0 1.8489857E-005 0 0 0 3.9193821E-005 0.0013415325 0 3.579149E-006 0 0 0 0 0.0055462269 3.7393232E-005 0 0 0 0.0032461 0.0015356557 0.0019915953 0.0015778632 0.0008546281 0.0021439553 0.0003157141 0.0037470482 +T>G GTC G[T>G]C 0.0002023656 4.7002381E-005 0.0045019853 0 0.0003277349 0.0016 0 0.0005248216 0.0006 0.002 0 0.0004 9.3373513E-005 0.0019 0.0022 0.0032 0.0090784615 9.20431E-007 0 0.0028305751 0.0006 0 0 0.0010736323 0 0.002460705 5.0790565E-005 0 0 0.001869 0.0007606153 0.0041116159 0.0032012845 0.0008454968 0.0013465618 0.0003570074 0.0027277577 +T>G GTG G[T>G]G 0.0011883532 0.0001099257 0.0163914526 0.0018 0.0059488798 0.001 0.0017 0.0060877535 0.005 0.0009 0.001 0.0011 1.0579194E-005 0.0012 0.0037 0.0008 0.0047827755 0.009695 0.0043 0.0027332194 0.0004 0.0018775892 0.0001871324 0.002924697 0.0086852444 0.0008172016 0.0047429186 0.0042178083 0.0036405938 0.0033445 0.0054079152 3.70860800590008E-020 0.002512037 0.0012687784 0.0077472793 0.0015192874 0.0082395121 +T>G GTT G[T>G]T 0.0008007233 8.647718E-005 0.0070672366 0.0002 0.0033074666 0.0035 0.0009 0.0054274338 0.0185 0.003 0 0.0032 5.3741207E-005 0.0038 0.019 0.0044 0.0634977566 0.0028905535 0.0025 0.0035585586 0.0008 0 0 0.0008250983 0.0027685717 0.0078335613 0.002298476 0.0316489973 0.0061810238 0.0056069 0.0101885638 0.0066566288 0.0079578565 0.0029254388 0.0018168896 0.0004726412 0.0032734591 +T>G TTA T[T>G]A 0.0013975537 0.000071737 0.0054271842 0 0.0052028744 0.0009 0 0.0017432214 0.0502 0.005 0 0.0019 0.0005465818 0 0 0.0068 0.0001334106 3.6318404E-005 0.0032 2.69147E-007 0 0.0016516988 0 0 0.0020814799 8.534935E-006 0.0011890225 0.0093896587 0 0.0086563 0.0008187477 0.000948451 0.0005293442 2.28346914246428E-020 0.0002407249 7.25392033429029E-005 0.0017254818 +T>G TTC T[T>G]C 0.001291737 1.4281456E-005 0.0061602504 0.0003 0.0051316079 0.0019 0.001 0.0025498383 0.0081 0.0092 0 0.0027 0.0002353471 0.0015 0.0004 0.0069 0.0096133452 0.003233838 0.0018 0.0003772344 0.0018 0 0 0 0.0005789788 0.0027185098 0.0002802954 0.030117077 0 0.0043282 0.0015336834 0.0010831046 0.0010211012 2.28346914246428E-020 0.0013929045 0.0003332825 0.0037135711 +T>G TTG T[T>G]G 0.0020310769 0.0002066152 0.0110765263 0.003 0.0060552541 0.0011 0.001 0.0060303952 0.0088 0.0022 0.0003 0.0011 0.000000479 0.0002 0.0009 0.0049 0.0045224623 0.0007546018 0.0011 0.0005154216 0.0003 0.002572752 0.0002475019 0.0013605049 0.0094291959 0.0013691612 0.0023530556 0.0126987508 0.000353696 0.0082628 0.0015835907 3.70860800590008E-020 0.003717572 2.28346914246428E-020 0.0039677318 0.0002233266 0.0022664664 +T>G TTT T[T>G]T 0.0040301282 2.3598204E-005 0.0130009842 0.0011 0.0133699358 0.0072 0.0014 0.0072239989 0.0545 0.0633 0.0003 0.0032 0.0006705883 0.0025 0.0033 0.0163 0.0580404078 0.0021264415 0.0013 0.0006156567 0.0003 0 0 6.9515778E-005 0.0078696716 0.0025680767 0.0001395613 0.2336597833 0.0061048341 0 0.0031734006 0.001871395 0.0032018465 2.28346914246428E-020 0.0014171235 0.0003757336 0.0024231362 diff -r 14fe7238c6d7 -r 916846f73e25 R/compareSignature_Galaxy.r --- a/R/compareSignature_Galaxy.r Thu Apr 28 03:59:27 2016 -0400 +++ b/R/compareSignature_Galaxy.r Fri Apr 29 05:11:28 2016 -0400 @@ -8,7 +8,7 @@ ######################################################################################################################################### -# Compare new signatures with published one using the cosine similarity method # +# Compare new sigantures with published one using the cosine similarity method # ######################################################################################################################################### diff -r 14fe7238c6d7 -r 916846f73e25 hg18_listAVDB.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg18_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,32 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space +#characters are TAB characters): +# +# +# +# +# +#hg18_refGene.txt g +#hg18_genomicSuperDups.txt r +#hg18_snp138.txt f +hg18_refGene.txt g +hg18_knownGene.txt g +hg18_ensGene.txt g +hg18_cytoBand.txt r +hg18_gwasCatalog.txt r +hg18_genomicSuperDups.txt r +hg18_snp138.txt f +hg18_ALL.sites.2014_10.txt f +hg18_AFR.sites.2014_10.txt f +hg18_AMR.sites.2014_10.txt f +hg18_EAS.sites.2014_10.txt f +hg18_EUR.sites.2014_10.txt f +hg18_SAS.sites.2014_10.txt f +hg18_esp6500siv2_all.txt f +hg18_esp6500siv2_aa.txt f +hg18_esp6500siv2_ea.txt f +hg18_ljb26_sift.txt f +hg18_ljb26_pp2hdiv.txt f +hg18_ljb26_pp2hvar.txt f +hg18_cosmic70.txt f +hg18_exac03.txt f diff -r 14fe7238c6d7 -r 916846f73e25 hg19_listAVDB.txt --- a/hg19_listAVDB.txt Thu Apr 28 03:59:27 2016 -0400 +++ b/hg19_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -29,9 +29,11 @@ hg19_ljb26_sift.txt f hg19_ljb26_pp2hdiv.txt f hg19_ljb26_pp2hvar.txt f +hg19_ljb26_mt.txt f hg19_cosmic70.txt f hg19_exac03.txt f hg19_exac03nontcga.txt f hg19_exac03nonpsych.txt f hg19_kaviar20150923.txt f hg19_hrcr1.txt f +hg19_dbscsnv11.txt f diff -r 14fe7238c6d7 -r 916846f73e25 hg38_listAVDB.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg38_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,36 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg38_listAVDB.txt has this format (white space +#characters are TAB characters): +# +# +# +# +# +#hg38_refGene.txt g +#hg38_genomicSuperDups.txt r +#hg38_snp142.txt f +hg38_refGene.txt g +hg38_knownGene.txt g +hg38_cytoBand.txt r +hg38_gwasCatalog.txt r +hg38_genomicSuperDups.txt r +hg38_snp142.txt f +hg38_ALL.sites.2015_08.txt f +hg38_AFR.sites.2015_08.txt f +hg38_AMR.sites.2015_08.txt f +hg38_EAS.sites.2015_08.txt f +hg38_EUR.sites.2015_08.txt f +hg38_SAS.sites.2015_08.txt f +hg38_esp6500siv2_all.txt f +hg38_esp6500siv2_aa.txt f +hg38_esp6500siv2_ea.txt f +hg38_ljb26_sift.txt f +hg38_ljb26_pp2hdiv.txt f +hg38_ljb26_pp2hvar.txt f +hg38_cosmic70.txt f +hg38_exac03.txt f +hg38_exac03nontcga.txt f +hg38_exac03nonpsych.txt f +hg38_kaviar20150923.txt f +hg38_hrcr1.txt f +hg38_dbscsnv11.txt f \ No newline at end of file diff -r 14fe7238c6d7 -r 916846f73e25 mm10_listAVDB.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mm10_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,17 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The mm10_listAVDB.txt has this format (white space +#characters are TAB characters): +# +# +# +# +# +#mm10_refGene.txt g +#mm10_genomicSuperDups.txt r +#mm10_snp137.txt f +mm10_refGene.txt g +mm10_knownGene.txt g +mm10_ensGene.txt g +mm10_cytoBand.txt r +mm10_genomicSuperDups.txt r +mm10_snp142.txt f diff -r 14fe7238c6d7 -r 916846f73e25 mutspecAnnot.pl --- a/mutspecAnnot.pl Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecAnnot.pl Fri Apr 29 05:11:28 2016 -0400 @@ -38,7 +38,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -our $max_cpu = 1; # Max number of CPU to use for the annotation +our $max_cpu = 12; # Max number of CPU to use for the annotation # Recover the current path diff -r 14fe7238c6d7 -r 916846f73e25 mutspecAnnot.xml --- a/mutspecAnnot.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecAnnot.xml Fri Apr 29 05:11:28 2016 -0400 @@ -33,7 +33,6 @@ - + - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecCompare.xml --- a/mutspecCompare.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecCompare.xml Fri Apr 29 05:11:28 2016 -0400 @@ -109,11 +109,22 @@ - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecFilter.pl --- a/mutspecFilter.pl Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecFilter.pl Fri Apr 29 05:11:28 2016 -0400 @@ -45,7 +45,7 @@ # Zero databases is specified if( ($dbSNP == 0) && ($segDup == 0) && ($esp == 0) && ($thG == 0) ) { - print STDERR "There is no databases selected for filtering against!!!\nPlease choose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; + print STDERR "There is no databases selected for filtering against!!!\nPlease chose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; exit; } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecFilter.xml --- a/mutspecFilter.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecFilter.xml Fri Apr 29 05:11:28 2016 -0400 @@ -97,11 +97,22 @@ - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecNmf.xml --- a/mutspecNmf.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecNmf.xml Fri Apr 29 05:11:28 2016 -0400 @@ -108,11 +108,22 @@ - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecNmf_wrapper.sh --- a/mutspecNmf_wrapper.sh Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecNmf_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=1 +cpu=8 @@ -13,7 +13,7 @@ source=$1;shift input=$1 -if [[ $source == "html" ]] +if [[ $source == "html" ]] then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt fi @@ -44,7 +44,7 @@ else echo "
" >> $html echo "
" >> $html -fi +fi echo "" >> $html echo "" >> $html diff -r 14fe7238c6d7 -r 916846f73e25 mutspecSplit.xml --- a/mutspecSplit.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecSplit.xml Fri Apr 29 05:11:28 2016 -0400 @@ -85,11 +85,22 @@ - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecStat.xml --- a/mutspecStat.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecStat.xml Fri Apr 29 05:11:28 2016 -0400 @@ -156,11 +156,22 @@ - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } diff -r 14fe7238c6d7 -r 916846f73e25 mutspecStat_wrapper.sh --- a/mutspecStat_wrapper.sh Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecStat_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=1 +cpu=8 @@ -119,9 +119,9 @@ touch $outEstimateSign echo "Estimating the number of signatures
" >> $html echo "

Computed statistics for estimating the number of signatures


" >> $outEstimateSign - echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF.
+ echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF.
Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing,
- Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point.
+ Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point.
Frigyesi et al. 2008, considered the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data.

The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate.

The original data are shuffled for comparing the quality measures obtained with our data (Data x) and from randomized data (Data y). The curves for the actual data are in solid line, those for the randomized data are in dashed line.

" >> $outEstimateSign diff -r 14fe7238c6d7 -r 916846f73e25 rn6_listAVDB.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rn6_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,14 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space +#characters are TAB characters): +# +# +# +# +# +#rn6_refGene.txt g +#rn6_genomicSuperDups.txt r +#rn6_snp138.txt f +rn6_refGene.txt g +rn6_ensGene.txt g +rn6_snp146.txt f \ No newline at end of file diff -r 14fe7238c6d7 -r 916846f73e25 tool_dependencies.xml --- a/tool_dependencies.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 29 05:11:28 2016 -0400 @@ -3,8 +3,8 @@ $REPOSITORY_INSTALL_DIR - - + + @@ -43,7 +43,7 @@ - +