mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 41 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 66.7% | 53.3 / 32.8 | 30 | 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 | 1 | . | G | 65.5% | 52.2 / 32.4 | 30 | 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 | 57.9% | 54.8 / 146.1 | 126 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 56.3% | 3.2 / 142.9 | 119 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.8% | 62.6 / 240.1 | 168 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 45.5% | 10.0 / 17.4 | 45 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 41.7% | 12.5 / 14.6 | 38 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 3,323,603 | 0 | T | G | 40.6% | 11.9 / 10.4 | 34 | D97A (GAC→GCC) | PP_2923 | hypothetical protein |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 39.5% | 15.1 / 10.4 | 38 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 36.2% | 72.5 / 10.5 | 49 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 35.7% | 132.8 / 117.1 | 130 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 117,279 | 0 | G | T | 33.3% | 78.2 / 16.1 | 45 | intergenic (+59/+35) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 32.5% | 25.0 / 11.1 | 41 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 31.7% | 47.4 / 10.5 | 47 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 6,008,725 | 0 | G | C | 31.4% | 140.0 / 18.9 | 70 | R258P (CGC→CCC) | ydcJ | metalloprotein |
| * | NC_002947_CJ‑RC | 648,237 | 0 | T | G | 30.0% | 50.9 / 11.6 | 40 | intergenic (+6/+85) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947_CJ‑RC | 1,641,265 | 0 | G | T | 27.1% | 110.5 / 10.8 | 50 | F142L (TTC→TTA) | cmoA | tRNA 5‑methoxyuridine(34)/uridine‑5‑oxyacetic acid(34) metyltransferase CmoA |
| * | NC_002947_CJ‑RC | 4,864,260 | 0 | A | C | 26.4% | 118.4 / 12.3 | 53 | Y1106D (TAC→GAC) | smc | chromosome partition protein Smc |
| * | NC_002947_CJ‑RC | 6,008,735 | 0 | G | C | 26.3% | 186.8 / 15.1 | 76 | P261P (CCG→CCC) | ydcJ | metalloprotein |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 25.7% | 87.4 / 29.3 | 35 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 33 (0.420) | 15 (0.200) | 15/280 | 5.3 | 32.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 30 (0.400) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 14 (0.180) +GCC |
13/284 | 6.0 | 87.7% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.090) | 12 (0.200) | 8/220 | 6.3 | 27.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 58 (0.980) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 12 (0.150) | 16 (0.220) | 10/268 | 6.7 | 51.5% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 19 (0.260) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 60 (0.770) | 9 (0.140) +29 bp |
7/232 | 7.1 | 24.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809865 | 10 (0.130) | intergenic (‑271/‑284) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 1419549 = | 35 (0.450) | 5 (0.080) | 5/232 | 8.1 | 18.9% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 1419637 = | 15 (0.240) | intergenic (‑126/+10) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 26 (0.330) | 4 (0.070) | 4/220 | 8.4 | 23.7% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 6 (0.100) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | = 5861679 | 35 (0.450) | 4 (0.060) | 4/230 | 8.7 | 12.3% | intergenic (+42/+96) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein |
| ? | NC_002947_CJ‑RC | = 5861724 | 29 (0.470) | intergenic (+87/+51) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | 1731163 = | 29 (0.370) | 4 (0.060) | 4/234 | 8.8 | 16.2% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947_CJ‑RC | 1731255 = | 18 (0.280) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947_CJ‑RC | = 414021 | 43 (0.550) | 4 (0.060) | 4/234 | 8.8 | 11.0% | intergenic (+41/‑162) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947_CJ‑RC | = 414051 | 30 (0.470) | intergenic (+71/‑132) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||