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 39 shown, sorted by frequency from high to low) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 57.0% | 33.8 / 130.7 | 107 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,353,299 | 0 | C | A | 55.6% | 3.0 / 10.1 | 9 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
* | NC_002947_CJ‑RC | 4,952,675 | 0 | T | G | 53.8% | ‑3.3 / 10.2 | 14 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
* | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.2% | 34.7 / 185.9 | 129 | 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 | 41.7% | 123.9 / 155.1 | 132 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 2,101,751 | 0 | A | C | 40.4% | 24.6 / 20.2 | 55 | L186R (CTG→CGG) | PP_1878 | hypothetical protein |
* | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 37.5% | 10.5 / 18.0 | 16 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 36.5% | 44.5 / 13.4 | 54 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
* | NC_002947_CJ‑RC | 856,598 | 0 | G | C | 34.1% | 80.4 / 13.0 | 44 | intergenic (+28/+88) | pagL‑I/PP_0738 | lipid A 3‑O‑deacylase/hypothetical protein |
* | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 34.0% | 40.2 / 12.9 | 55 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
* | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 33.3% | 16.4 / 12.9 | 15 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
* | NC_002947_CJ‑RC | 4,648,341 | 0 | A | C | 32.7% | 85.8 / 11.5 | 52 | V302G (GTG→GGG) | PP_4112 | sulfate transporter |
* | NC_002947_CJ‑RC | 1,625,208 | 0 | A | C | 32.0% | 12.1 / 10.9 | 25 | intergenic (+31/+26) | PP_1425/nadB | hypothetical protein/L‑aspartate oxidase |
* | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 31.6% | 23.0 / 11.5 | 19 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 31.6% | 19.9 / 13.3 | 19 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,743,289 | 0 | C | A | 31.6% | 32.1 / 10.2 | 19 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 31.0% | 108.0 / 12.7 | 58 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
* | NC_002947_CJ‑RC | 5,194,439 | 1 | . | G | 30.8% | 12.1 / 13.9 | 13 | intergenic (+117/‑85) | PP_4572/PP_4573 | hypothetical protein/AAA family ATPase |
* | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 30.0% | 80.3 / 33.0 | 40 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
* | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 30.0% | 79.1 / 31.4 | 40 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
Marginal new junction evidence (lowest skew 10 of 42 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.090) | 21 (0.360) | 14/220 | 5.0 | 49.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991750 | 38 (0.650) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 17 (0.220) +GCC |
14/284 | 6.9 | 94.5% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
* | ? | NC_002947_CJ‑RC | = 652782 | 59 (0.760) | 13 (0.190) | 10/250 | 7.5 | 33.8% | 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 | = 4809882 | 4 (0.050) | 9 (0.130) | 7/250 | 9.0 | 24.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991764 | 52 (0.780) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | 4895256 = | 21 (0.270) | 5 (0.080) | 5/236 | 9.8 | 22.2% | intergenic (+28/‑180) | pyk/PP_4302 | pyruvate kinase/urea transporter |
? | NC_002947_CJ‑RC | 4895335 = | 18 (0.290) | intergenic (+107/‑101) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
* | ? | NC_002947_CJ‑RC | = 2957080 | 38 (0.490) | 7 (0.090) | 7/280 | 9.9 | 14.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947_CJ‑RC | 2957165 = | 46 (0.610) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947_CJ‑RC | = 5684230 | 3 (0.040) | 7 (0.090) +CGGG |
7/282 | 10.0 | 70.6% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
? | NC_002947_CJ‑RC | 5684231 = | 3 (0.040) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
* | ? | NC_002947_CJ‑RC | 6003718 = | 37 (0.480) | 4 (0.070) | 4/230 | 10.2 | 13.5% | intergenic (+10/+99) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase |
? | NC_002947_CJ‑RC | 6003812 = | 22 (0.360) | intergenic (+104/+5) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase | |||||
* | ? | NC_002947_CJ‑RC | = 3947940 | 20 (0.260) | 5 (0.080) | 4/234 | 10.4 | 24.3% | coding (109/1797 nt) | PP_3483 | type II secretion system protein |
? | NC_002947_CJ‑RC | = 3947969 | 15 (0.240) | coding (80/1797 nt) | PP_3483 | type II secretion system protein | |||||
* | ? | NC_002947_CJ‑RC | 5384101 = | 21 (0.270) | 3 (0.050) | 3/220 | 10.6 | 20.7% | intergenic (+18/+115) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
? | NC_002947_CJ‑RC | 5384199 = | 7 (0.120) | intergenic (+116/+17) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |