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 43 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 | 170,833 | 0 | A | G | 56.2% | ‑6.4 / 13.1 | 16 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 53.3% | ‑1.4 / 29.1 | 48 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,558,407 | 0 | G | T | 53.3% | 6.6 / 20.2 | 15 | intergenic (‑68/+103) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 52.2% | 3.4 / 22.4 | 23 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 51.6% | 22.5 / 43.8 | 31 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 49.4% | 5.8 / 124.5 | 85 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.2% | 60.2 / 187.2 | 132 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 47.8% | 45.9 / 159.4 | 111 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 358,091 | 0 | G | A | 46.2% | 1.7 / 10.6 | 14 | intergenic (+59/‑71) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 44.4% | ‑1.3 / 10.6 | 9 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 358,090 | 0 | T | C | 42.9% | 0.9 / 13.2 | 14 | intergenic (+58/‑72) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 40.5% | 62.5 / 94.7 | 91 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 358,094 | 0 | A | G | 40.0% | 4.4 / 13.1 | 15 | intergenic (+62/‑68) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 37.2% | 32.7 / 14.5 | 53 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 37.0% | 20.3 / 14.1 | 30 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 36.2% | 88.5 / 11.4 | 47 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 358,085 | 0 | A | G | 35.3% | 11.5 / 12.6 | 17 | intergenic (+53/‑77) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947_CJ‑RC | 358,087 | 0 | C | T | 35.3% | 14.8 / 10.7 | 17 | intergenic (+55/‑75) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 34.3% | 33.9 / 28.0 | 36 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 358,096 | 0 | C | T | 33.3% | 17.3 / 10.9 | 18 | intergenic (+64/‑66) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| 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 | 4809877 = | 5 (0.070) | 20 (0.390) | 14/222 | 3.9 | 50.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 36 (0.700) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 34 (0.500) | 17 (0.260) | 17/282 | 4.5 | 34.4% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 32 (0.490) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 17 (0.260) +GCC |
16/286 | 4.9 | 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 | = 4586136 | 11 (0.160) | 19 (0.310) | 12/270 | 5.8 | 54.9% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 21 (0.340) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 5 (0.070) | 10 (0.160) | 9/268 | 6.9 | 27.9% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 47 (0.760) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 11 (0.160) | 9 (0.140) | 8/278 | 7.6 | 48.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 9 (0.140) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 2472140 | 21 (0.310) | 5 (0.100) | 4/214 | 8.0 | 22.1% | intergenic (+44/+105) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | = 2472186 | 20 (0.410) | intergenic (+90/+59) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 36 (0.530) | 7 (0.110) | 7/276 | 8.1 | 15.4% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 43 (0.680) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 867920 = | 16 (0.240) | 6 (0.100) | 6/266 | 8.3 | 27.5% | intergenic (+18/+159) | PP_0750/mqo‑I | hypothetical protein/malate:quinone oxidoreductase |
| ? | NC_002947_CJ‑RC | 868010 = | 17 (0.280) | intergenic (+108/+69) | PP_0750/mqo‑I | hypothetical protein/malate:quinone oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 6 (0.090) | 7 (0.110) | 6/268 | 8.4 | 23.9% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | 5789298 = | 39 (0.630) | intergenic (+26/‑105) | PP_5068/trxC | hypothetical protein/thioredoxin | |||||