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 33 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 | 5,558,423 | 2 | . | C | 100.0% | 18.8 / NA | 7 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0% | 19.0 / NA | 7 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 64.0% | 46.5 / 29.6 | 26 | 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 | 64.0% | 40.9 / 29.9 | 26 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 62.5% | ‑5.4 / 11.8 | 16 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 668,080 | 0 | G | T | 58.8% | 7.7 / 19.4 | 17 | intergenic (+44/+108) | yfhM/PP_0571 | lipoprotein/membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 57.6% | ‑3.2 / 31.4 | 36 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,455,917 | 0 | G | A | 52.9% | ‑1.2 / 13.8 | 20 | intergenic (+115/‑240) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| * | NC_002947_CJ‑RC | 3,466,843 | 0 | C | G | 52.6% | 0.9 / 12.5 | 19 | intergenic (‑18/+106) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 170,839 | 0 | T | G | 52.4% | 8.3 / 25.4 | 21 | intergenic (+20/‑550) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.3% | 41.3 / 183.0 | 128 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.1% | ‑3.5 / 183.9 | 133 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 50.0% | ‑0.5 / 11.2 | 26 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,455,911 | 0 | G | T | 50.0% | 5.1 / 15.7 | 22 | intergenic (+109/‑246) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 46.3% | 62.5 / 168.5 | 121 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 43.5% | 19.4 / 18.8 | 51 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 37.6% | 112.1 / 123.6 | 126 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 37.2% | 18.0 / 10.4 | 45 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,196,590 | 0 | T | G | 36.7% | 17.0 / 13.6 | 32 | intergenic (+29/+24) | PP_4574/PP_4575 | hypothetical protein/urea amidolyase‑like protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 31.8% | 38.3 / 11.3 | 44 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| Marginal new junction evidence (lowest skew 10 of 51 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 27 (0.330) | 18 (0.220) | 18/282 | 5.8 | 37.1% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 35 (0.440) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 13 (0.170) | 13/268 | 7.0 | 30.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 56 (0.740) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.080) | 10 (0.160) | 9/222 | 7.3 | 26.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 49 (0.780) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 10 (0.120) | 12 (0.150) | 11/278 | 8.2 | 48.5% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 16 (0.200) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 63 (0.760) | 11 (0.140) | 10/276 | 8.5 | 14.8% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 67 (0.850) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.020) | 10 (0.120) +GCC |
9/286 | 9.3 | 83.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.020) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 7 (0.100) | 7/252 | 9.3 | 17.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 65 (0.910) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 8 (0.100) | 11 (0.140) | 8/268 | 9.3 | 23.3% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 65 (0.850) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 1419549 = | 14 (0.170) | 4 (0.060) | 4/234 | 10.6 | 26.5% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 1419637 = | 11 (0.170) | intergenic (‑126/+10) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5916999 | 24 (0.290) | 6 (0.090) | 4/236 | 10.7 | 25.9% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | = 5917039 | 15 (0.220) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||