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 23 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 2,380,341 | 0 | G | A | 36.3% | 131.9 / 43.9 | 91 | intergenic (+31/‑72) | yfbL/yfbM | putative peptidase/DUF1877 family protein |
| * | CP009273 | 4,137,073 | 0 | A | C | 35.3% | 71.4 / 11.1 | 52 | Y3S (TAC→TCC) | frwD | putative enzyme IIB component of PTS |
| * | CP009273 | 3,199,794 | 0 | C | T | 31.8% | 112.9 / 25.1 | 64 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | CP009273 | 2,319,929 | 0 | T | G | 31.5% | 178.9 / 13.0 | 92 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | CP009273 | 1,472,581 | 0 | T | G | 28.4% | 158.4 / 10.7 | 74 | G33G (GGT→GGG) | ynbB | putative CDP‑diglyceride synthase |
| * | CP009273 | 3,659,062 | 0 | C | A | 26.9% | 188.3 / 29.2 | 93 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | CP009273 | 4,034,021 | 0 | G | A | 26.1% | 56.7 / 26.9 | 46 | intergenic (+25/+245) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| * | CP009273 | 3,659,058 | 0 | T | C | 24.2% | 169.9 / 16.8 | 93 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | CP009273 | 3,406,257 | 0 | C | T | 24.0% | 147.9 / 21.2 | 75 | A190T (GCC→ACC) | acrS | acrAB operon transcriptional repressor |
| * | CP009273 | 2,380,362 | 0 | C | T | 23.7% | 205.6 / 24.5 | 97 | intergenic (+52/‑51) | yfbL/yfbM | putative peptidase/DUF1877 family protein |
| * | CP009273 | 4,351,352 | 0 | A | G | 23.4% | 111.3 / 11.0 | 64 | S134P (TCC→CCC) | cadC | cadBA operon transcriptional activator |
| * | CP009273 | 3,659,044 | 0 | G | A | 23.4% | 197.1 / 22.3 | 94 | R43* (CGA→TGA) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | CP009273 | 5,162 | 0 | T | A | 23.1% | 157.5 / 16.1 | 65 | intergenic (+142/‑72) | thrC/yaaX | L‑threonine synthase/DUF2502 family putative periplasmic protein |
| * | CP009273 | 173,606 | 0 | G | A | 23.1% | 137.9 / 14.3 | 65 | S169F (TCC→TTC) | yadS | UPF0126 family inner membrane protein |
| * | CP009273 | 1,009,465 | 0 | G | T | 23.1% | 184.8 / 10.3 | 65 | D251Y (GAT→TAT) | pqiB | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| * | CP009273 | 4,526,014 | 0 | A | T | 22.8% | 231.6 / 25.3 | 92 | intergenic (+166/+417) | yjhR/nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| * | CP009273 | 2,999,331 | 0 | A | T | 21.3% | 169.4 / 17.9 | 76 | intergenic (‑186/‑290) | ygeV/ygeW | putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase |
| * | CP009273 | 357,394 | 0 | C | T | 21.0% | 168.8 / 15.0 | 81 | E60K (GAA→AAA) | lacA | thiogalactoside acetyltransferase |
| * | CP009273 | 1,819,288 | 0 | C | T | 20.9% | 160.1 / 14.0 | 67 | intergenic (‑94/+109) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| * | CP009273 | 4,020,593 | 0 | T | A | 20.9% | 159.5 / 11.5 | 67 | intergenic (+5/+376) | fre/fadA | NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase (thiolase I) |
| Marginal new junction evidence (lowest skew 10 of 37 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | Exported | 923 = | 373 (0.010) | 142 (0.010) +29 bp |
33/172 | 1.5 | 7.7% | intergenic (‑131/‑88) | aadA/fdh | aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag |
| ? | KX077536 | 1006 = | 4187 (1.270) | intergenic (–/‑93) | –/unknown | –/BLA | |||||
| * | ? | Exported | = 905 | 1373 (0.030) | 53 (0.000) +AAATGCTAAAATTCCAC |
31/190 | 1.6 | 2.0% | intergenic (‑113/‑106) | aadA/fdh | aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag |
| ? | KX077536 | 4030 = | 4640 (1.410) | intergenic (+631/‑74) | unknown/unknown | transposase/cbbM | |||||
| * | ? | CP009273 | = 4161761 | 18 (0.260) | 14 (0.010) +C |
8/228 | 2.7 | 4.8% | intergenic (+77/‑224) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 24 = | 541 (0.160) | intergenic (–/‑1075) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | = 4161759 | 19 (0.270) | 11 (0.010) +C |
7/228 | 2.8 | 4.0% | intergenic (+75/‑226) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 22 = | 516 (0.160) | intergenic (–/‑1077) | –/unknown | –/BLA | |||||
| * | ? | KX077536 | = 3121 | NA (NA) | 142 (0.040) +TGGA |
4/210 | 3.1 | NA | coding (703/981 nt) | unknown | transposase |
| ? | KX077536 | 3122 = | NA (NA) | coding (704/981 nt) | unknown | transposase | |||||
| * | ? | CP009273 | = 3054218 | 56 (0.800) | 1472 (0.880) | 5/228 | 3.1 | 36.5% | coding (10/2145 nt) | scpA | methylmalonyl‑CoA mutase |
| ? | KX077536 | = 964 | 5065 (1.550) | intergenic (–/‑135) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | = 4161774 | 23 (0.330) | 7 (0.000) +T |
4/228 | 3.2 | 1.4% | intergenic (+90/‑211) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 37 = | 1003 (0.300) | intergenic (–/‑1062) | –/unknown | –/BLA | |||||
| * | ? | Exported | 1 = | 0 (0.000) | 23 (0.000) +TGTCTAAC |
3/214 | 3.3 | 0.97% | coding (792/792 nt) | aadA | aminoglycoside adenylyltransferase (Murphy, 1985) |
| ? | KX077536 | = 965 | 5071 (1.540) | intergenic (–/‑134) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | 3054202 = | 58 (0.830) | 13 (0.000) | 5/214 | 5.3 | 32.5% | intergenic (+197/‑7) | argP/scpA | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor/methylmalonyl‑CoA mutase |
| ? | Exported | 9 = | 0 (0.000) | coding (784/792 nt) | aadA | aminoglycoside adenylyltransferase (Murphy, 1985) | |||||
| * | ? | CP009273 | 3124276 = | NA (NA) | 4 (0.060) | 4/226 | 6.0 | NA | coding (740/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | CP009273 | 3359335 = | NA (NA) | noncoding (775/1195 nt) | IS5 | repeat region | |||||