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 26 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 | 74.4% | 82.0 / 30.1 | 40 | 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 | 71.4% | 71.6 / 29.8 | 40 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 56.5% | 3.5 / 24.4 | 25 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 54.4% | 29.2 / 160.4 | 125 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.0% | 51.3 / 261.3 | 186 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 170,839 | 0 | T | G | 52.6% | 1.4 / 17.8 | 20 | intergenic (+20/‑550) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 51.8% | ‑2.1 / 28.7 | 29 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 50.0% | ‑2.7 / 22.4 | 40 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 46.3% | 19.6 / 16.7 | 44 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 46.3% | 64.5 / 210.6 | 149 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 41.5% | 22.2 / 12.4 | 43 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 40.0% | 53.9 / 17.0 | 46 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,541,374 | 0 | G | C | 39.5% | 59.9 / 10.2 | 38 | intergenic (+49/+72) | PP_4871/PP_4872 | lysine decarboxylase family protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 38.6% | 24.3 / 12.1 | 46 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,001,196 | 0 | A | T | 31.9% | 92.4 / 13.4 | 71 | Q58L (CAG→CTG) | PP_0863 | hypothetical protein |
| * | NC_002947_CJ‑RC | 441,318 | 0 | T | G | 31.4% | 74.2 / 12.2 | 51 | W67G (TGG→GGG) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 4,242,229 | 0 | T | G | 25.3% | 170.6 / 13.1 | 75 | D203A (GAC→GCC) | PP_3719 | putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 117,248 | 0 | C | A | 25.0% | 158.8 / 12.4 | 60 | intergenic (+28/+66) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 5,941,834 | 0 | T | A | 24.7% | 192.6 / 11.2 | 97 | L527Q (CTA→CAA) | rbbA | ribosome‑associated ATPase |
| * | NC_002947_CJ‑RC | 4,051,262 | 0 | A | C | 24.6% | 139.7 / 11.8 | 69 | intergenic (+26/+17) | oprB‑III/PP_3571 | carbohydrate‑selective porin/acetylornithine deacetylase |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.100) | 23 (0.340) | 16/220 | 5.9 | 50.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 38 (0.550) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 70 (0.780) | 18 (0.230) | 18/250 | 6.3 | 37.4% | 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 | = 5558423 | 3 (0.030) | 26 (0.290) +GCC |
20/284 | 6.7 | 89.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.070) | 16 (0.190) | 16/266 | 7.5 | 32.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 60 (0.720) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.070) | 12 (0.150) | 12/250 | 8.5 | 29.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 53 (0.680) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.450) | 13 (0.150) | 13/280 | 9.1 | 19.8% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 66 (0.760) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.100) | 9 (0.120) | 8/238 | 10.0 | 23.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 52 (0.700) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.020) | 11 (0.130) +CGGG |
10/282 | 10.6 | 85.0% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 37 (0.410) | 4 (0.060) | 3/212 | 12.4 | 13.3% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 25 (0.380) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 2078256 | 21 (0.230) | 6 (0.080) | 5/256 | 12.6 | 22.8% | intergenic (+41/+74) | PP_1853/PP_1854 | LysR family transcriptional regulator/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2078303 | 22 (0.280) | intergenic (+88/+27) | PP_1853/PP_1854 | LysR family transcriptional regulator/hypothetical protein | |||||