# HG changeset patch
# User greg
# Date 1697219864 0
# Node ID 3275d4866650d9502ad87ac532ab984fb051060f
Uploaded
diff -r 000000000000 -r 3275d4866650 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Fri Oct 13 17:57:44 2023 +0000
@@ -0,0 +1,12 @@
+name: cfsan_snp_pipeline_call_consensus_snps
+owner: greg
+description: Call the consensus base for a sample at the specified positions where high-
+ confidence SNPs were previously called in any of the samples.
+long_description: Call the consensus base for a sample at the specified positions where high-
+ confidence SNPs were previously called in any of the samples. Generates a single-sequence
+ fasta file with one base per specified position.
+categories:
+- Metagenomics
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/snp_pipeline/cfsan_snp_pipeline_call_consensus_snps
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r 3275d4866650 cfsan_snp_pipeline_call_consensus_snps.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_snp_pipeline_call_consensus_snps.xml Fri Oct 13 17:57:44 2023 +0000
@@ -0,0 +1,59 @@
+
+
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `_
+ ]]>
+
+
+
diff -r 000000000000 -r 3275d4866650 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 13 17:57:44 2023 +0000
@@ -0,0 +1,17 @@
+
+ 2.2.1
+ 0
+ 21.01
+
+
+ snp-pipeline
+ python
+
+
+
+
+ 10.7717/peerj-cs.20
+
+
+
+
diff -r 000000000000 -r 3275d4866650 test-data/input_call_pileup.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_call_pileup.pileup Fri Oct 13 17:57:44 2023 +0000
@@ -0,0 +1,48502 @@
+gi|9626243|ref|NC_001416.1| 1 G 0 * *
+gi|9626243|ref|NC_001416.1| 2 G 0 * *
+gi|9626243|ref|NC_001416.1| 3 G 0 * *
+gi|9626243|ref|NC_001416.1| 4 C 0 * *
+gi|9626243|ref|NC_001416.1| 5 G 1 . 0
+gi|9626243|ref|NC_001416.1| 6 G 0 * *
+gi|9626243|ref|NC_001416.1| 7 C 1 . 6
+gi|9626243|ref|NC_001416.1| 8 G 0 * *
+gi|9626243|ref|NC_001416.1| 9 A 1 . B
+gi|9626243|ref|NC_001416.1| 10 C 1 . =
+gi|9626243|ref|NC_001416.1| 11 C 0 * *
+gi|9626243|ref|NC_001416.1| 12 T 0 * *
+gi|9626243|ref|NC_001416.1| 13 C 0 * *
+gi|9626243|ref|NC_001416.1| 14 G 1 . 4
+gi|9626243|ref|NC_001416.1| 15 C 1 . 8
+gi|9626243|ref|NC_001416.1| 16 G 1 . F
+gi|9626243|ref|NC_001416.1| 17 G 2 .^K. :>
+gi|9626243|ref|NC_001416.1| 18 G 3 ... ;=>
+gi|9626243|ref|NC_001416.1| 19 T 3 ... AGA
+gi|9626243|ref|NC_001416.1| 20 T 1 . G
+gi|9626243|ref|NC_001416.1| 21 T 2 N. 9A
+gi|9626243|ref|NC_001416.1| 22 T 3 ... 714
+gi|9626243|ref|NC_001416.1| 23 C 2 .. =0
+gi|9626243|ref|NC_001416.1| 24 G 1 . ;
+gi|9626243|ref|NC_001416.1| 25 C 4 .... A?>8
+gi|9626243|ref|NC_001416.1| 26 T 3 ... 75;
+gi|9626243|ref|NC_001416.1| 27 A 4 .... 19:?
+gi|9626243|ref|NC_001416.1| 28 T 4 .... 16E?
+gi|9626243|ref|NC_001416.1| 29 T 4 .... 29D>
+gi|9626243|ref|NC_001416.1| 30 T 4 .... 8D?0
+gi|9626243|ref|NC_001416.1| 31 A 3 ... F9A
+gi|9626243|ref|NC_001416.1| 32 T 4 .... =8/<
+gi|9626243|ref|NC_001416.1| 33 G 3 ... FH2
+gi|9626243|ref|NC_001416.1| 34 A 2 .. A@
+gi|9626243|ref|NC_001416.1| 35 A 2 .. G9
+gi|9626243|ref|NC_001416.1| 36 A 5 ....^K. :C209
+gi|9626243|ref|NC_001416.1| 37 A 3 ... ;=D
+gi|9626243|ref|NC_001416.1| 38 T 6 ...... @09;48
+gi|9626243|ref|NC_001416.1| 39 T 3 ... /C0
+gi|9626243|ref|NC_001416.1| 40 T 4 .... AF?B
+gi|9626243|ref|NC_001416.1| 41 T 1 . >
+gi|9626243|ref|NC_001416.1| 42 C 6 .....^K. =C90C<
+gi|9626243|ref|NC_001416.1| 43 C 7 ....... E=>2.H/
+gi|9626243|ref|NC_001416.1| 44 G 2 .. A4
+gi|9626243|ref|NC_001416.1| 45 G 4 .... BC?;
+gi|9626243|ref|NC_001416.1| 46 T 4 .... .09=
+gi|9626243|ref|NC_001416.1| 47 T 6 ...... C73=;7
+gi|9626243|ref|NC_001416.1| 48 T 5 ..... 6;GCC
+gi|9626243|ref|NC_001416.1| 49 A 6 ...... FHC0?G
+gi|9626243|ref|NC_001416.1| 50 A 5 ....^K. 7FG1=
+gi|9626243|ref|NC_001416.1| 51 G 5 ..... >9274
+gi|9626243|ref|NC_001416.1| 52 G 5 ....^K. >6G;;
+gi|9626243|ref|NC_001416.1| 53 C 8 ........ 8;<29:B=
+gi|9626243|ref|NC_001416.1| 54 G 5 ..... /@81;
+gi|9626243|ref|NC_001416.1| 55 T 6 ...... 8G0F<;
+gi|9626243|ref|NC_001416.1| 56 T 4 .... G<5>
+gi|9626243|ref|NC_001416.1| 57 T 5 ..... 6:84155
+gi|9626243|ref|NC_001416.1| 59 C 6 ...... ;91>45
+gi|9626243|ref|NC_001416.1| 60 G 8 ........ :.?CDB>F
+gi|9626243|ref|NC_001416.1| 61 T 9 .......^K.^K. 7/:1G@AB=
+gi|9626243|ref|NC_001416.1| 62 T 7 ....... <63@C13
+gi|9626243|ref|NC_001416.1| 63 C 5 ..... :E=5F
+gi|9626243|ref|NC_001416.1| 64 T 7 ....N.. .:C14:.
+gi|9626243|ref|NC_001416.1| 65 T 9 ......... 42F;0:GE=
+gi|9626243|ref|NC_001416.1| 66 C 6 ...... F46G0C
+gi|9626243|ref|NC_001416.1| 67 T 9 ......... DFE3>F33C
+gi|9626243|ref|NC_001416.1| 68 T 10 .........^K. 8/FCF?672
+gi|9626243|ref|NC_001416.1| 71 T 8 ........ FE;GB9
+gi|9626243|ref|NC_001416.1| 72 C 8 ........ G8DC==2A
+gi|9626243|ref|NC_001416.1| 73 A 6 ...... .9?>E4
+gi|9626243|ref|NC_001416.1| 74 T 6 ...... 26HC/.
+gi|9626243|ref|NC_001416.1| 75 A 10 .......... 19=2G0>6?4
+gi|9626243|ref|NC_001416.1| 76 A 9 ......... E51.4H36?
+gi|9626243|ref|NC_001416.1| 77 C 10 .......... >1.3B4F;HH
+gi|9626243|ref|NC_001416.1| 78 T 7 ....... 34E<@B@
+gi|9626243|ref|NC_001416.1| 79 T 9 ......... /622EH9B0
+gi|9626243|ref|NC_001416.1| 80 A 9 ......... EG>BBBB;.
+gi|9626243|ref|NC_001416.1| 81 A 6 ...... A;7ABH
+gi|9626243|ref|NC_001416.1| 82 T 8 ........ 6B/7/F.<
+gi|9626243|ref|NC_001416.1| 83 G 5 ..... G7;/D
+gi|9626243|ref|NC_001416.1| 84 T 10 .......... /<8AH
+gi|9626243|ref|NC_001416.1| 87 T 11 ........... E=84026?7>7
+gi|9626243|ref|NC_001416.1| 88 T 10 ...$....... A;5F?:>9.C
+gi|9626243|ref|NC_001416.1| 89 A 8 ........ >=?D6
+gi|9626243|ref|NC_001416.1| 92 T 11 ..........^K. 48H.@BC:=91
+gi|9626243|ref|NC_001416.1| 93 A 9 ......... =A5/ED@?B
+gi|9626243|ref|NC_001416.1| 94 A 13 ............. GD7.56D1;@6<6
+gi|9626243|ref|NC_001416.1| 95 A 11 ........... 4BE0@1>4:EB
+gi|9626243|ref|NC_001416.1| 96 A 10 .......... C.718@<.H@
+gi|9626243|ref|NC_001416.1| 97 T 11 ..........^K. B>9F7>824HA
+gi|9626243|ref|NC_001416.1| 98 A 15 ............... 5DE@HEC1>1;6F=G
+gi|9626243|ref|NC_001416.1| 99 C 12 ............ .>.A77197=.5
+gi|9626243|ref|NC_001416.1| 100 C 8 ........ 5@4G7/BB
+gi|9626243|ref|NC_001416.1| 101 C 8 ........ 8D9F6G;B
+gi|9626243|ref|NC_001416.1| 102 T 9 ......... =?D:81:C3
+gi|9626243|ref|NC_001416.1| 103 C 10 .......... HH813.0.88
+gi|9626243|ref|NC_001416.1| 104 T 11 ........... /.3738=.<1B
+gi|9626243|ref|NC_001416.1| 105 G 11 ..$......C.. 53E.=B2;1/D
+gi|9626243|ref|NC_001416.1| 106 A 9 ........^K, 19E:E0:F7
+gi|9626243|ref|NC_001416.1| 107 A 11 .........., 2;=E28/2G/.
+gi|9626243|ref|NC_001416.1| 108 A 10 ........., 2AA75D4A87
+gi|9626243|ref|NC_001416.1| 109 A 9 .N....... 7;8.62=44
+gi|9626243|ref|NC_001416.1| 110 G 12 ..........,. F@<9>01DE2
+gi|9626243|ref|NC_001416.1| 111 A 11 .....$....,. DF08>:A719.
+gi|9626243|ref|NC_001416.1| 112 A 11 ........... =19:3FE1DH0
+gi|9626243|ref|NC_001416.1| 113 A 11 .........,. 1>A=3CG56;5
+gi|9626243|ref|NC_001416.1| 114 G 10 .NA.....,. F:18@@>6FD
+gi|9626243|ref|NC_001416.1| 115 G 15 ......N.....,.^K. >=G74G/64EAA74A
+gi|9626243|ref|NC_001416.1| 116 A 10 .......... 5A12
+gi|9626243|ref|NC_001416.1| 117 A 9 .......,. D<7B3H6E4
+gi|9626243|ref|NC_001416.1| 118 A 10 .......... 23941@256>
+gi|9626243|ref|NC_001416.1| 119 C 11 .........,. ?3DGEA3AAE8
+gi|9626243|ref|NC_001416.1| 120 G 10 ........,. E?7=9=H3=4
+gi|9626243|ref|NC_001416.1| 121 A 9 .$........ <8A;;9:7B
+gi|9626243|ref|NC_001416.1| 122 C 12 ..........,. /FG9B498:3=2
+gi|9626243|ref|NC_001416.1| 123 A 7 ....,.. 3HC:F4>
+gi|9626243|ref|NC_001416.1| 124 G 10 ........,. 99=0@8/:36
+gi|9626243|ref|NC_001416.1| 125 G 8 ........ 0;2H;GFE
+gi|9626243|ref|NC_001416.1| 126 T 8 ........ G5?08A>H
+gi|9626243|ref|NC_001416.1| 127 G 5 ..... 992HC
+gi|9626243|ref|NC_001416.1| 128 C 8 ........ G8<:36<.
+gi|9626243|ref|NC_001416.1| 129 T 9 ......... 6<EC.9?=
+gi|9626243|ref|NC_001416.1| 132 A 11 ........... 49?23?.<@=D
+gi|9626243|ref|NC_001416.1| 133 A 12 .......,.... C=D2D<9;?H29
+gi|9626243|ref|NC_001416.1| 134 G 10 ......,... B3D<;A?
+gi|9626243|ref|NC_001416.1| 136 G 9 ......,.. 6.>D=082?
+gi|9626243|ref|NC_001416.1| 137 A 11 ......,.... 5D4EA08A?GD
+gi|9626243|ref|NC_001416.1| 138 G 10 .......... 4F61@09D<1
+gi|9626243|ref|NC_001416.1| 139 G 9 .......n. 3:E/BAA7;
+gi|9626243|ref|NC_001416.1| 140 C 6 ....G. >@6=;E
+gi|9626243|ref|NC_001416.1| 141 T 11 .......,... 0AA189B;5@9
+gi|9626243|ref|NC_001416.1| 142 T 13 N........,... CD.?3@B.3D0?4
+gi|9626243|ref|NC_001416.1| 143 T 11 .......,... G4HB0G7;553
+gi|9626243|ref|NC_001416.1| 144 T 12 .......,.... E=0H9.:F>><.
+gi|9626243|ref|NC_001416.1| 145 T 11 ........,.. 9/>FF@HA5>8
+gi|9626243|ref|NC_001416.1| 146 G 10 ..T....,.. H5.B6=GF6<
+gi|9626243|ref|NC_001416.1| 147 G 10 N......... DD7D<7A2D7
+gi|9626243|ref|NC_001416.1| 148 C 9 .......,. ?=FA2=6A@
+gi|9626243|ref|NC_001416.1| 149 C 9 .......,. @996F1;=.
+gi|9626243|ref|NC_001416.1| 150 T 9 .....,... A5:>D.488
+gi|9626243|ref|NC_001416.1| 151 C 10 .....,.... =?:55350F>
+gi|9626243|ref|NC_001416.1| 152 T 13 ........,.$... DH=7C>?A6A9BA
+gi|9626243|ref|NC_001416.1| 153 G 8 ......,. B@;53D.5
+gi|9626243|ref|NC_001416.1| 154 T 14 .......,....^K.^K. :H@69@9?4HG.E?
+gi|9626243|ref|NC_001416.1| 155 C 12 .....N...... 4299GA2E>7HE
+gi|9626243|ref|NC_001416.1| 156 G 12 ........,... 0?HC9E?F=G0A
+gi|9626243|ref|NC_001416.1| 157 T 10 .........^K. ?A@=CB8=F8
+gi|9626243|ref|NC_001416.1| 158 T 14 .C.....,...... 3?11G9G5H4/A27
+gi|9626243|ref|NC_001416.1| 159 T 12 .$........... @0.@1/4>=5F:
+gi|9626243|ref|NC_001416.1| 160 C 13 ...N...,..... .70..279299CF
+gi|9626243|ref|NC_001416.1| 161 C 14 ............,^K, :B:5E.1<.:4CD/
+gi|9626243|ref|NC_001416.1| 162 T 11 ...N,.....^K. A6>>C?;58.>
+gi|9626243|ref|NC_001416.1| 163 T 10 .......N^K.^K, 582B/2A@>0
+gi|9626243|ref|NC_001416.1| 164 T 13 .........,.., 1H?0B?;366=>0
+gi|9626243|ref|NC_001416.1| 165 C 14 .....,...,,.,^K. >H/44E=4<>35DE
+gi|9626243|ref|NC_001416.1| 166 T 16 ......,......,.. C5FFE044/7;
+gi|9626243|ref|NC_001416.1| 168 T 12 ....n....,,. .FF
+gi|9626243|ref|NC_001416.1| 169 G 18 .......,.....,,.,. 61C7=3.>2A>8BHG=;.
+gi|9626243|ref|NC_001416.1| 170 T 12 ..........,. 7E??D<7220:G
+gi|9626243|ref|NC_001416.1| 171 T 11 .....,..,,. @H0:DA2G7D1
+gi|9626243|ref|NC_001416.1| 172 T 13 ...........,, /DH644?F:54A?
+gi|9626243|ref|NC_001416.1| 173 T 16 ............,.,. 54EEEB965C2=EF?G
+gi|9626243|ref|NC_001416.1| 174 T 15 ...,.........,. >:;00.=9821?/?4
+gi|9626243|ref|NC_001416.1| 175 G 14 .........,,.,. 32;12?.C7821B1
+gi|9626243|ref|NC_001416.1| 176 T 14 ..........,,,. 2A?E5E;G7>@>/8
+gi|9626243|ref|NC_001416.1| 177 C 14 ......,..,..,. 2E13@AD/G/H2C@
+gi|9626243|ref|NC_001416.1| 178 C 14 ....,.....,.,. /A6:8=B80E8>..B
+gi|9626243|ref|NC_001416.1| 183 A 17 ...........,...,, 4=H@729A99H15@@;6
+gi|9626243|ref|NC_001416.1| 184 A 16 ....,......,,... :8A;CB0?@A;:8=D/
+gi|9626243|ref|NC_001416.1| 185 T 19 ......,.....,..,... 67AA<=FG.1D4;CDB?@<
+gi|9626243|ref|NC_001416.1| 186 G 20 ....,......,,.A,..,, .;E5==6:C9.D58>4>@3E
+gi|9626243|ref|NC_001416.1| 187 A 16 ....,.....,...., 2=0>@HC<8.050;98
+gi|9626243|ref|NC_001416.1| 188 A 19 ......$......,....,, >7G3DAA1G7A055.A@89
+gi|9626243|ref|NC_001416.1| 189 C 18 .....,.......,..., /HH>>G7..BBG6FA545
+gi|9626243|ref|NC_001416.1| 190 A 19 ....,.....,.,..,,,^), 047GGB949?A:D4B2G3@
+gi|9626243|ref|NC_001416.1| 191 A 14 ....,.....,,,, :G3<41@>?3C88@
+gi|9626243|ref|NC_001416.1| 192 T 19 ..N....,........,,, B/.7@;74HH6DG0C86?=
+gi|9626243|ref|NC_001416.1| 193 G 16 ..........,..,,, 5988EG5565G6497=
+gi|9626243|ref|NC_001416.1| 194 G 20 ....,......,....,,.^K, H?F83>7BHBFDBE2:AG41
+gi|9626243|ref|NC_001416.1| 195 A 21 ..........,n..,..,,,. H:C>;A5G;H>HB=?0
+gi|9626243|ref|NC_001416.1| 196 A 24 ......,......,.....,,,., 3AC.><8<2@05=F;@5>@2F2;:
+gi|9626243|ref|NC_001416.1| 197 G 17 ....,..,,....,,., /BC51=?H=HDH74;CE
+gi|9626243|ref|NC_001416.1| 198 T 20 ..........,,...,,.,^K, A=9=7?54D5G/19634H3.
+gi|9626243|ref|NC_001416.1| 199 C 17 ........,....,,,, 9;>56>28BH5H@4.E6
+gi|9626243|ref|NC_001416.1| 200 A 20 ...$,.....,..,,,.,,.^K. H;=;4:8D82./247E34F0
+gi|9626243|ref|NC_001416.1| 201 A 16 ...,,,.,..,,,,.^K, ;>92D1?6CED7./?4
+gi|9626243|ref|NC_001416.1| 202 C 17 .....,,.,..,,..,^K. 3EH:F679H=857@9H9
+gi|9626243|ref|NC_001416.1| 203 A 22 ........,,....,,,.,.,. :2G9FBB?392FD2C:>AE186
+gi|9626243|ref|NC_001416.1| 204 A 22 .....,....$.,..,..,,,,. <@>9HDH0700@:B@5;14E
+gi|9626243|ref|NC_001416.1| 206 A 18 .,.....,...,,,.,.. 44;G45D56C0@H97<0C
+gi|9626243|ref|NC_001416.1| 207 A 21 ...,...,,.$,..,,,,,.., =;?55;.E>=2HG5@4B==??
+gi|9626243|ref|NC_001416.1| 208 G 16 ...,.,,.,,,,..,. H54AA510/.;CG@B6
+gi|9626243|ref|NC_001416.1| 209 C 23 ...,.....,....,,,.n..,. D==.C15C>9E;G@7;29=HA1B
+gi|9626243|ref|NC_001416.1| 210 A 16 ..,.....,,,,,.,, 97C4HGE5?>F@4C.;E.2=06E
+gi|9626243|ref|NC_001416.1| 212 C 25 ..,....,.,..,,,,,,.,.,.., H=;07?BAF=9;;1/GC;E??4=99
+gi|9626243|ref|NC_001416.1| 213 T 22 ......N,,.,.,,,,.,.G., 2/G?H8C9FD6>B7H:0A=:0A@
+gi|9626243|ref|NC_001416.1| 218 G 24 ........,,.,...,,,.,,.., 5AD;7DB0@B<:AEH/@C.>4:=/
+gi|9626243|ref|NC_001416.1| 219 A 27 ..,.....,,.,..,,,,,,.,.,.,. 320C:=G87.25B:85;>A=E5BF7H8
+gi|9626243|ref|NC_001416.1| 220 C 23 ...........,,.,.,.,.... 1DH@=3D795<:H9=114H1A7H
+gi|9626243|ref|NC_001416.1| 221 A 18 .....,..,,,,,,.,.^K. 0BA2=C4DB7EH@F?C1D
+gi|9626243|ref|NC_001416.1| 222 T 29 .....,....,,,..,,,.,,.,..,... >0/?HFF185=28@5F>:G/G@484<.69HA
+gi|9626243|ref|NC_001416.1| 224 T 20 .......,.,..,,,,.... /GH:F29@8CH44E1/45;D
+gi|9626243|ref|NC_001416.1| 225 T 22 ........N,..,,,,,.,.,. 04/D7@4310=G85AG:=G7?9
+gi|9626243|ref|NC_001416.1| 226 C 24 ........,,..,,.,.,N..,.. 57=HE=B./A40;?>E6HG=AC@2
+gi|9626243|ref|NC_001416.1| 227 G 21 ...,.....,..,a,..,,.. =A:GE20=>
+gi|9626243|ref|NC_001416.1| 229 T 22 ....,.....,.,.,,..,... =64D436A@/=DC6<0;B8>0=
+gi|9626243|ref|NC_001416.1| 230 G 24 ...,.......,..,,,..,.,.. 18?6?/>EC;FD=H?=06EB;60H
+gi|9626243|ref|NC_001416.1| 231 C 26 ..,.....,,,$...,,.,.,.,.,.. A920F9A.122A7;>.906E:FCD:/
+gi|9626243|ref|NC_001416.1| 232 G 26 ....,.....,..,,,,.,..,.... 0@FB/=G=B7782>4.66@906.C27
+gi|9626243|ref|NC_001416.1| 233 A 25 ....,..,,...,,,.,.,.,.... :>/E9@C58G8E26G7:F=.>C:5.
+gi|9626243|ref|NC_001416.1| 234 G 22 ..........,.,,.,..,... 8@=2A5.<6EH7@9;BGC/9E
+gi|9626243|ref|NC_001416.1| 236 A 24 ...,..,....,,,,,.,..,... 349F21@:B4DH6C9
+gi|9626243|ref|NC_001416.1| 237 T 31 ....,......,...,,,.,,..,......^K, @98C?F>@:..B6/DG0HB6?@;;9H.:/7@
+gi|9626243|ref|NC_001416.1| 238 C 24 .........,,...,,,.,..... 63E/@.CF0>5@3@FG08A81DF0
+gi|9626243|ref|NC_001416.1| 239 C 23 ...,....,,..,,,.,....., ;CD@<567C@FB61@EE1726/3
+gi|9626243|ref|NC_001416.1| 240 G 24 ..,.....,.,,,.,N,.,..,.. 31E?D>4H>@DG=H?D2AD;.EE0
+gi|9626243|ref|NC_001416.1| 241 T 29 ...,.$.$...,....,.,,.,.,..,.... >9HEEE<G51.7?>./C=4C>D.5D
+gi|9626243|ref|NC_001416.1| 242 A 29 .....,...,,...,,,,,....,...., 3A0;610:B/.FGD;B/@/36?B8E58>H=74DC;=83DH@B/B10
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+gi|9626243|ref|NC_001416.1| 416 G 27 c....,..N,,..,..,,.,.,,,,.. 8/8E79@1/B07.4001=0546;@A?5
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+gi|9626243|ref|NC_001416.1| 419 C 26 ,....,...,,....,,,.,,,,.,. ;2;?8?25/=2.9B?369.B<1C7@<
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+gi|9626243|ref|NC_001416.1| 421 C 27 ,..,,.,.,.,.,,.,,,.,,.,..., A:18=1:/A6@8;3?D3.GA;1GH9
+gi|9626243|ref|NC_001416.1| 422 C 27 ,...,,..,,,,..,$,.,,,,.,,.., :B>@B?6C?C4>>E435=9CB6/0D4:
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+gi|9626243|ref|NC_001416.1| 424 G 25 ,...,..,,.,.,.,,,,$,,....^K. 0H96F?90GH18;>>H>E<:2DHC:
+gi|9626243|ref|NC_001416.1| 425 C 27 ,..,,..,,..,.,,.,,,.,.,..,. H0@@H?>59H2>B:5<.C=7CA7C2>@
+gi|9626243|ref|NC_001416.1| 426 C 23 ,....,,...,..,..,,,,... BDG@041.3FD.75=F./<.;E4
+gi|9626243|ref|NC_001416.1| 427 A 29 ,..,,...,,..,...,,.,,,.,..,.. C;30.B5/3@=;=.4G;A=8=3@F:4AD9
+gi|9626243|ref|NC_001416.1| 428 G 22 ,..,,..,..,,,,,...,..^K, /G0CDC7GBDF4/;45;.=F10
+gi|9626243|ref|NC_001416.1| 429 G 24 ,...,.,,.,...,.,,,.,.,.. E?6/@C<9@9014C8/B>G@BBF9/<3.
+gi|9626243|ref|NC_001416.1| 433 T 27 ,...,...,.,..,,,,,.,,..,.,, 1<331H@D66A1F1HB3B=@DC@A;.8
+gi|9626243|ref|NC_001416.1| 434 A 32 ,..,...,,..,...,,.,,,.,.,.,..,,^K. G.>;D899F>0AEFAB1A:..;3<2D1>@71E
+gi|9626243|ref|NC_001416.1| 435 T 28 ,..,,..,,...$.,,.,,,,...,.,,. ?G@25CDB7BC>491A<>/DF5HF5B8C
+gi|9626243|ref|NC_001416.1| 436 T 24 ..,.$..,,.n..,,..,,.,..,, ?G7>4=4D50/D4<@>5=3>DDG/
+gi|9626243|ref|NC_001416.1| 437 G 29 ....,,.,,.,.,.,,.,,...,..,..^K, .F4;A0:>H1/:C7/70A;2:.A0HB@/8
+gi|9626243|ref|NC_001416.1| 438 A 28 ,..,..,..,..,,.,,,,.......,. 0@771@==<7D448G/49D@A9A:A
+gi|9626243|ref|NC_001416.1| 441 A 25 ....,,,..,,,.,,.,..,..,., G7CB@D11C<:>>>>9571.GH64G
+gi|9626243|ref|NC_001416.1| 442 C 20 ..,,..,..,.,T,....,. ;4?82.4;D0F3;=2=<229
+gi|9626243|ref|NC_001416.1| 443 G 29 ,...,,..,,.T,,,n.,.,....,,.., 9/H?C87GA;@0;0F?@;;C=6>.G097.
+gi|9626243|ref|NC_001416.1| 444 A 25 ...,.,..,..,,,.,..,..,,.. BE>/09F7DE<05A/DG.F>>0@.C
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+gi|9626243|ref|NC_001416.1| 650 G 21 .,,,,,.,.,....,,..... B@B1;6E;3@:C/E6/A52D8
+gi|9626243|ref|NC_001416.1| 651 A 22 .,.,,,$,,,.,,....,,,... <.HCGA901.A0BH0@4B@F9@
+gi|9626243|ref|NC_001416.1| 652 T 23 ..,.,,,.,,..,.....,.... FHD7/@?=??<6=D9.D08:9./
+gi|9626243|ref|NC_001416.1| 653 A 26 ...,.,,$,.,,,,.,,..,..,,... ?;25;CABHGF=38/D194<;0.DB48
+gi|9626243|ref|NC_001416.1| 656 A 24 ...,.,.,,,,..,....,,.... E9050D4<0@??;367?1;:>B2E
+gi|9626243|ref|NC_001416.1| 657 T 21 .,,.,,,.,..,...,,.... /1FC03/;=8=FHG?;.326;;<..B8>6FH8:
+gi|9626243|ref|NC_001416.1| 659 A 19 ,,.,,,.,,....,..... @>;;50;8B:D<4<4/52?
+gi|9626243|ref|NC_001416.1| 660 A 19 .,,,..,,.....,..... >7<862@F8E18GGDBAD1
+gi|9626243|ref|NC_001416.1| 661 A 24 .,.,,,,.........,,...... 4@3G4F7>8=>C1>;CE927@69:
+gi|9626243|ref|NC_001416.1| 663 C 18 ...,,,.,,,,,...,., 10893A46@6B0@379?6
+gi|9626243|ref|NC_001416.1| 664 C 29 ...,.,,.,,.,,......,,......,^I. >8H>=EDF7;GGD2F87AG?0H66GF243
+gi|9626243|ref|NC_001416.1| 665 A 28 ...,,,.,,,,.,,.....,......,. B0654157150DC=GAGG94EH21:689
+gi|9626243|ref|NC_001416.1| 666 T 21 ....,,.,,....,,.....^K, 5@G96.CA
+gi|9626243|ref|NC_001416.1| 670 C 26 ..T,,,,,,,,......,,......, ?8944HG5.C5;<3C2?4A.9D00@?
+gi|9626243|ref|NC_001416.1| 671 A 24 .,..,,,,,..T.,,.....,.,, ;4791<7<61628?;9;;6<932B
+gi|9626243|ref|NC_001416.1| 672 A 24 .-3AGC.-3AGC,-3agc.-3AGC,-3agc,-3agc,$,-3agc,-3agc.-3AGC,-3agc.-3AGC.-3AGC.-3AGC,-3agc,-3agc.-3AGC.-3AGC.-3AGC.-3AGC.-3AGC.-3AGC,-3agc,-3agc 903618484/2/852065838962
+gi|9626243|ref|NC_001416.1| 673 A 2 ** 91
+gi|9626243|ref|NC_001416.1| 674 G 2 ** 91
+gi|9626243|ref|NC_001416.1| 675 C 2 ** 91
+gi|9626243|ref|NC_001416.1| 676 A 3 ,,, 91A
+gi|9626243|ref|NC_001416.1| 677 G 4 ,,,^K, B.=.
+gi|9626243|ref|NC_001416.1| 678 C 4 ,,,, D6=2
+gi|9626243|ref|NC_001416.1| 679 C 22 .,.,,.,,,.........,,,, 86;2D:77/0;:5:;;:7;;73
+gi|9626243|ref|NC_001416.1| 680 G 16 ..,,,,......,.,, >F83028>4;H55/BD
+gi|9626243|ref|NC_001416.1| 681 C 18 ,.,.,,,...,,....., 0F9E183;<59@9B;.6D
+gi|9626243|ref|NC_001416.1| 682 G 20 ..,.,.,,,..,,,...,,, 6>9C041:;98=45@2GH.?
+gi|9626243|ref|NC_001416.1| 683 C 27 ..,.,,,,,....,,,....,,,.,,^K, 6C/?10>67G4;79E7@94.79/>E26
+gi|9626243|ref|NC_001416.1| 684 T 22 ..,.,,.,,,$...,,....,., 6<4.F21:86E3GH.9::GFG:
+gi|9626243|ref|NC_001416.1| 685 G 22 ..,,.,,,...,....,,.,,, ;3:>C572@;H.9E34C>AC>H
+gi|9626243|ref|NC_001416.1| 686 G 21 ..,,,,C...,,....,,.,, C0>BA4/.H?>/DC@@2HHGC
+gi|9626243|ref|NC_001416.1| 687 A 25 ...,.,,,,...,,,...,.,.,^K.^K, ?@><8/:0CD88/:17EG2>ACH36
+gi|9626243|ref|NC_001416.1| 688 T 24 ..,,,,,,,....,,...,,.,^K.^K, 4/5<:/GD33>/7HD<4?28H./6=28H:HBF2F0F<7AB
+gi|9626243|ref|NC_001416.1| 691 A 25 .,,,,,,.....,,....,,,,,,. >6;@E=>?A;?D<@<7C30@62303
+gi|9626243|ref|NC_001416.1| 692 C 27 .,,,,.....,,,......,,.,..,. BHGBE78<760CAB66<0;8727.0@H
+gi|9626243|ref|NC_001416.1| 693 T 29 .,.,,,,.....,,,......,,,,.,., FF=H@BAC>G6@A66C/E;?2:0;=>.
+gi|9626243|ref|NC_001416.1| 694 G 25 ...,,....,,...,.,,,,.,.., ;;A/5D5061A.6A::AD:H.F/21
+gi|9626243|ref|NC_001416.1| 695 A 27 ..,,,,.....,.....,.,,,.,.,, 676/8:29CHB6F;B=D>.;.?9BHFF
+gi|9626243|ref|NC_001416.1| 696 T 26 ..,.,,,,...,,...,.,,,,,,., G71=?B03<@6G6?H05F@A479;
+gi|9626243|ref|NC_001416.1| 697 A 28 ...,,,,,.....,......,,,,,.., =EG;8789G0:D2>6/=F5ED3A21GC9
+gi|9626243|ref|NC_001416.1| 698 C 26 ..,.,,...,,,....,,.,,,.,., 6HA8B5:;/F.6A929C:DH/5;.H0
+gi|9626243|ref|NC_001416.1| 699 C 31 ..,.,,,,,.....,,,....,..,,.,.., H8C<>>?BC@BA>?A@@.0:D2BEE=460:<
+gi|9626243|ref|NC_001416.1| 700 G 30 .,,,,,.....,,,...$.,,,.,,,.,,.. ;4/FD4;7
+gi|9626243|ref|NC_001416.1| 701 G 27 ..,,,,...,,,...,,.,.,.,.,.. 4<>=3:CH/EGH4E49D1083C49;52
+gi|9626243|ref|NC_001416.1| 702 G 31 ..,,,,,.....,,,..,.,,.,,.,.,.,. 1219:E11?6?:HFH.3/78BHGE<.H=>40<<027F.B21
+gi|9626243|ref|NC_001416.1| 704 T 25 .,,,......,,...,..,,...,. DG21@:DAC89BDF<=D?>B7><;/
+gi|9626243|ref|NC_001416.1| 705 T 27 ..,,,,.....,,..,.,.,,,.,.,. .22EG>7HHG/.>.AH6GEE:990.?G
+gi|9626243|ref|NC_001416.1| 706 G 25 .,,,,,.....,,...,,,,..,.^K. 8C?83C14H?<;4=HD48A:=4??B
+gi|9626243|ref|NC_001416.1| 707 C 31 .,,,,,,,....,,..$.,,.,,.,.,....^K, =HD/<9D>.<80;:A3/=@>>;9.D3>FF@8
+gi|9626243|ref|NC_001416.1| 708 T 26 .,,,,G....,,..,..,,,.,...^K. 964.8;0H:CE632F2>:C:HBA4F:
+gi|9626243|ref|NC_001416.1| 709 G 30 .,,,,....,,..,.,.,,,.,..,...,. /82<659G@1FH@AC?<><>//760A=00A<95?/AD;AB?<08D
+gi|9626243|ref|NC_001416.1| 711 G 28 .,,,,,....,,.,,.,,.,,.,..,., .=@?>729<0GD;2<5B/73898F8@6A
+gi|9626243|ref|NC_001416.1| 712 T 30 ..,,,......,,..,.,,,.,.,.,.,., 12@/6:;;6H@C@B5;4A:62C:2A1;6D7
+gi|9626243|ref|NC_001416.1| 714 A 23 ..,,,,...,..,,,,.,..,,^K, 3D6BF61DA6/@6H:6F<:527A
+gi|9626243|ref|NC_001416.1| 715 A 22 ..,,,.T.T,,.,,..,...,^K, @9;?05/@A5H53D1.1.
<7>?E89/E6HD@45<0
+gi|9626243|ref|NC_001416.1| 720 T 29 .,,,,..,...,.,,,,.,,.,...,,,^K, .6D@85=4E4730H@41/C3EH0CBD?3E
+gi|9626243|ref|NC_001416.1| 721 C 30 ..,,,,..,,..,..,,,,.,.,.,.,,,^K, 4CGD>21C5
+gi|9626243|ref|NC_001416.1| 722 G 26 .,,,..,,..,..,,,.,..,,,,,, =H80E0HDH
+gi|9626243|ref|NC_001416.1| 723 A 23 .,,,.,,..,.,,,,..,,.,,, 3@68GA/1C@.@4G5H
+gi|9626243|ref|NC_001416.1| 724 A 21 .,,,,.,..,.,,....,,,, >?=:5H?CE7G@8H5H@/68E
+gi|9626243|ref|NC_001416.1| 725 C 29 ..,,,,,,,....,.n,.n..,G..,.,, B7=.45HDF=HCA?H2.3G80:@.FG7>A
+gi|9626243|ref|NC_001416.1| 726 A 28 ..,,,,,.,,..,,,,,.,.,.,.,,,, C.@:1720F
+gi|9626243|ref|NC_001416.1| 727 G 24 .,,,,,.,...,,,,....,,,,, =522C25A@G4?7;6C6DHAAH=>
+gi|9626243|ref|NC_001416.1| 728 T 25 ..,,,,.,,....,,..,.,.,,,, BH6=160GG:F1?C>6AG@F8D?4G
+gi|9626243|ref|NC_001416.1| 729 C 26 ,,,,,..,,...,.,,..,..,,,,, C6/5H1D:.AAB2