Mercurial > repos > jjjjia > cpo_prediction
diff summary.txt @ 0:917a05a03ac9 draft
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| author | jjjjia |
|---|---|
| date | Tue, 14 Aug 2018 17:18:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summary.txt Tue Aug 14 17:18:49 2018 -0400 @@ -0,0 +1,69 @@ +2018-08-10 20:59:10.151624 + +ID: ASDF +Assembly: ASDF + + + +~~~~~~~MLST summary~~~~~~~ +MLST determined species: Klebsiella pneumoniae + +MLST Details: +/home/jjjjia/testCases/cpoResults/contigs/BC11-Kpn005_S2.fa kpneumoniae 147 gapA(3) infB(4) mdh(6) pgi(1) phoE(7) rpoB(4) tonB(38) + +MLST information: +!!!MLST determined species is NOT the same as expected species, contamination? mislabeling? + + + +~~~~~~~~Plasmids~~~~~~~~ + +predicted plasmid origins: +;IncFIB;IncFII;ColRNAI_rep_cluster_1987;rep_cluster_1195;ColRNAI_rep_cluster_1987,rep_cluster_2050 + +definitely plasmid contigs +00031;00019;00025;00035;00038;00039 + +likely plasmid contigs +00054;00033;00061;00062;00040;00063;00021;00050;00027;00052;00032;00045;00048;00047;00060;00049;00064;00029;00036;00028 + +mob-suite prediction details: +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00054_len=1680_cov=99.4_corr=0_spades=NODE_54_length_1680_cov_99.397296_pilon 1680 Incomplete KY271404 0.0163307 KU736877 IS3 3097.0 9280.0 10959.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00033_len=7099_cov=71.4_corr=0_spades=NODE_33_length_7099_cov_71.391566_pilon 7099 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00061_len=1290_cov=63.7_corr=0_spades=NODE_61_length_1290_cov_63.717111_pilon 1290 Incomplete KY271404 0.0163307 CP001182 IS6 1733.0 45808.0 46813.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00062_len=1261_cov=94.7_corr=0_spades=NODE_62_length_1261_cov_94.707231_pilon 1261 Incomplete KY271404 0.0163307 EU327987 IS91 1790.0 1.0 1167.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00040_len=4267_cov=45.7_corr=0_spades=NODE_40_length_4267_cov_45.722222_pilon 4267 Incomplete KY271404 0.0163307 MF168946 IS3 1055.0 57274.0 58321.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00063_len=1231_cov=111.8_corr=0_spades=NODE_63_length_1231_cov_111.776268_pilon 1231 Incomplete KY271404 0.0163307 MG764534 Tn3 1792.0 123.0 1353.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00021_len=50545_cov=56.2_corr=0_spades=NODE_21_length_50545_cov_56.199215_pilon 50545 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00050_len=2206_cov=232.0_corr=0_spades=NODE_50_length_2206_cov_232.019240_pilon 2206 Incomplete KY271404 0.0163307 MF344564 ISNCY 4047.0 26.0 2231.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00027_len=23176_cov=57.2_corr=1_spades=NODE_27_length_23176_cov_57.154584_pilon 23176 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00052_len=1916_cov=74.5_corr=0_spades=NODE_52_length_1916_cov_74.495808_pilon 1916 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00031_len=9290_cov=61.3_corr=0_spades=NODE_31_length_9290_cov_61.312889_pilon 9290 Incomplete IncFIB 000107__CP014778_00094 KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00032_len=8550_cov=90.1_corr=0_spades=NODE_32_length_8550_cov_90.057224_pilon 8550 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00045_len=2914_cov=67.7_corr=0_spades=NODE_45_length_2914_cov_67.672049_pilon 2914 Incomplete KY271404 0.0163307 EU780013 IS5 1230.0 22192.0 23343.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00048_len=2286_cov=54.9_corr=0_spades=NODE_48_length_2286_cov_54.938861_pilon 2286 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00047_len=2438_cov=67.3_corr=0_spades=NODE_47_length_2438_cov_67.279100_pilon 2438 Incomplete KY271404 0.0163307 KF306092 IS30 2737.0 3022.0 4503.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00060_len=1334_cov=206.0_corr=0_spades=NODE_60_length_1334_cov_205.993372_pilon 1334 Incomplete KY271404 0.0163307 KX710093 Tn3 1941.0 21.0 1353.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00049_len=2226_cov=74.2_corr=0_spades=NODE_49_length_2226_cov_74.201048_pilon 2226 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00019_len=68857_cov=55.7_corr=0_spades=NODE_19_length_68857_cov_55.651782_pilon 68857 Incomplete IncFII 000132__HG969996,000113__CP022035 MOBF NC_021231_00058 KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00064_len=1218_cov=229.8_corr=0_spades=NODE_64_length_1218_cov_229.791017_pilon 1218 Incomplete KY271404 0.0163307 MF344562 IS3 2250.0 381.0 1598.0 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00025_len=33717_cov=69.1_corr=0_spades=NODE_25_length_33717_cov_69.149628_pilon 33717 Incomplete IncFIB 000097__NC_025166_00051 KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00029_len=19880_cov=51.1_corr=0_spades=NODE_29_length_19880_cov_51.127221_pilon 19880 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00036_len=5070_cov=128.9_corr=0_spades=NODE_36_length_5070_cov_128.854744_pilon 5070 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 770 BC11-Kpn005_S2.fa|contig00028_len=20810_cov=52.4_corr=0_spades=NODE_28_length_20810_cov_52.435285_pilon 20810 Incomplete KY271404 0.0163307 +BC11-Kpn005_S2.fa 190 BC11-Kpn005_S2.fa|contig00035_len=5334_cov=187.2_corr=0_spades=NODE_35_length_5334_cov_187.195698_pilon 5334 Incomplete ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_019986_00002,NC_001848_00006 CP018444 0.00038558099999999997 +BC11-Kpn005_S2.fa 2088 BC11-Kpn005_S2.fa|contig00038_len=4444_cov=185.7_corr=0_spades=NODE_38_length_4444_cov_185.662497_pilon 4444 Incomplete rep_cluster_1195 000483__CP010949_00006 KY454616 0.00985499 +BC11-Kpn005_S2.fa novel_0 BC11-Kpn005_S2.fa|contig00039_len=4290_cov=125.7_corr=0_spades=NODE_39_length_4290_cov_125.717752_pilon 4290 Incomplete ColRNAI_rep_cluster_1987,rep_cluster_2050 000019__CP000651_00005,001473__CP024541 CP018739 0.061583900000000004 + + + +~~~~~~~~AMR Genes~~~~~~~~ + +predicted carbapenamase Genes: +OXA-181(plasmid) +other RGI AMR Genes: + +Details about the carbapenamase Genes: +/home/jjjjia/testCases/cpoResults/contigs/BC11-Kpn005_S2.fa contig00038 256 1053 OXA-181 1-798/798 =============== 0/0 100.0 100.0 bccdc AEP16366.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-181 + +Details about the RGI AMR Genes: