mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0% | 10.8 / NA | 5 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 59.3% | 37.3 / 37.8 | 27 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 59.3% | 44.2 / 37.4 | 27 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 58.8% | 33.9 / 93.5 | 85 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 56.5% | 8.4 / 137.3 | 108 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,905,987 | 0 | G | T | 55.6% | 4.4 / 10.0 | 9 | intergenic (‑136/‑132) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,712,093 | 0 | T | A | 53.3% | 1.6 / 13.5 | 16 | intergenic (+84/‑174) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 43.0% | 52.8 / 99.2 | 80 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,544,359 | 0 | C | G | 29.2% | 40.8 / 11.4 | 24 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 5,196,590 | 0 | T | G | 28.6% | 6.6 / 11.7 | 21 | intergenic (+29/+24) | PP_4574/PP_4575 | hypothetical protein/urea amidolyase‑like protein |
| * | NC_002947_CJ‑RC | 6,008,721 | 0 | A | C | 28.6% | 52.5 / 12.9 | 35 | T257P (ACC→CCC) | ydcJ | metalloprotein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 26.1% | 29.6 / 12.9 | 24 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,844,607 | 1 | . | G | 25.0% | 17.0 / 11.0 | 12 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 248,861 | 0 | C | A | 24.5% | 114.5 / 10.6 | 49 | Q148K (CAA→AAA) | PP_0198 | putative transporter |
| * | NC_002947_CJ‑RC | 1,438,934 | 0 | C | A | 23.1% | 87.2 / 15.6 | 40 | A246S (GCC→TCC) | yveA | aspartate‑proton symporter |
| * | NC_002947_CJ‑RC | 1,438,942 | 0 | G | T | 23.1% | 92.2 / 14.7 | 39 | A243E (GCG→GAG) | yveA | aspartate‑proton symporter |
| * | NC_002947_CJ‑RC | 2,282,774 | 0 | G | C | 22.7% | 38.2 / 10.2 | 22 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 22.7% | 38.8 / 10.0 | 22 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 4 (0.080) | 16 (0.410) | 8/222 | 4.2 | 59.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 19 (0.490) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.790) | 7 (0.140) | 7/282 | 6.0 | 17.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 29 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 31 (0.610) | 6 (0.140) | 5/252 | 6.3 | 31.0% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.020) | 6 (0.120) +CGGG |
6/284 | 6.5 | 86.1% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.020) | 7 (0.140) +GCC |
6/286 | 6.5 | 87.7% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.020) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.100) | 7 (0.150) | 5/268 | 6.6 | 30.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 27 (0.580) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 2472102 = | 19 (0.370) | 3 (0.080) | 3/214 | 6.6 | 14.7% | intergenic (+6/+143) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472226 = | 21 (0.560) | intergenic (+130/+19) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 1311718 | 15 (0.290) | 4 (0.080) | 4/282 | 7.5 | 15.8% | intergenic (‑186/+92) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA |
| ? | NC_002947_CJ‑RC | 1311803 = | 28 (0.570) | intergenic (‑271/+7) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA | |||||
| * | ? | NC_002947_CJ‑RC | 1107899 = | 56 (1.100) | 3 (0.060) | 3/266 | 7.8 | 5.4% | intergenic (+4/+112) | hisC/PP_0968 | histidinol‑phosphate aminotransferase/hypothetical protein |
| ? | NC_002947_CJ‑RC | 1108003 = | 55 (1.190) | intergenic (+108/+8) | hisC/PP_0968 | histidinol‑phosphate aminotransferase/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 3379748 = | 66 (1.300) | 3 (0.060) | 3/270 | 7.9 | 4.9% | coding (401/972 nt) | tnpS | cointegrate resolution protein S |
| ? | NC_002947_CJ‑RC | 3379857 = | 56 (1.190) | coding (292/972 nt) | tnpS | cointegrate resolution protein S | |||||