mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 380,012 | 1 | . | G | 67.7% | 76.3 / 40.2 | 34 | intergenic (‑131/+57) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| * | NC_000913 | 2,386,862 | 0 | G | A | 65.0% | 3.9 / 13.9 | 20 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 1,037,137 | 0 | A | G | 64.3% | ‑0.9 / 10.5 | 14 | E130G (GAG→GGG) | hyaF | hydrogenase‑1 protein nickel incorporation factor |
| * | NC_000913 | 1,037,140 | 0 | A | G | 64.3% | 3.7 / 11.3 | 14 | D131G (GAC→GGC) | hyaF | hydrogenase‑1 protein nickel incorporation factor |
| * | NC_000913 | 1,037,130 | 0 | T | A | 63.6% | 1.3 / 10.2 | 13 | L128M (TTG→ATG) | hyaF | hydrogenase‑1 protein nickel incorporation factor |
| * | NC_000913 | 3,578,287 | 0 | T | C | 61.1% | 7.4 / 17.3 | 18 | E147G (GAA→GGA) | gntR | d‑gluconate inducible gluconate regulon transcriptional repressor |
| * | NC_000913 | 3,599,408 | 0 | A | C | 61.1% | 12.2 / 17.2 | 18 | V84G (GTG→GGG) | livJ | branched‑chain amino acid ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,953,550 | 0 | A | C | 61.1% | 6.3 / 18.7 | 18 | T25P (ACC→CCC) | ilvD | dihydroxyacid dehydratase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 59.3% | 6.1 / 28.2 | 27 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 501,564 | 0 | A | C | 58.8% | 8.6 / 17.1 | 17 | *559E (TAA→GAA) | ybaL | inner membrane putative NAD(P)‑binding transporter |
| * | NC_000913 | 3,953,555 | 0 | A | G | 58.8% | 10.7 / 17.4 | 19 | G26G (GGA→GGG) | ilvD | dihydroxyacid dehydratase |
| * | NC_000913 | 1,079,468 | 0 | A | G | 57.1% | 4.2 / 12.7 | 14 | D55G (GAT→GGT) | putP | proline:sodium symporter |
| * | NC_000913 | 1,622,815 | 0 | C | A | 57.1% | ‑2.0 / 10.8 | 14 | intergenic (+74/+145) | yneM/dgcZ | inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing |
| * | NC_000913 | 1,622,816 | 0 | G | A | 57.1% | ‑6.3 / 12.6 | 14 | intergenic (+75/+144) | yneM/dgcZ | inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing |
| * | NC_000913 | 3,637,360 | 0 | G | A | 57.1% | 0.9 / 11.6 | 14 | F17F (TTC→TTT) | yhiN | putative oxidoreductase |
| * | NC_000913 | 3,637,366 | 0 | A | C | 56.2% | 8.7 / 18.4 | 16 | G15G (GGT→GGG) | yhiN | putative oxidoreductase |
| * | NC_000913 | 2,578,143 | 0 | A | C | 55.6% | 9.2 / 19.8 | 18 | L79V (TTA→GTA) | maeB | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| * | NC_000913 | 2,745,089 | 0 | A | C | 55.6% | 18.6 / 29.3 | 27 | V84G (GTG→GGG) | trmD | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| * | NC_000913 | 4,279,468 | 0 | C | G | 55.6% | 14.9 / 26.3 | 18 | G330G (GGC→GGG) | ghxP | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| * | NC_000913 | 2,578,068 | 0 | T | C | 53.8% | 9.6 / 14.2 | 13 | I104V (ATT→GTT) | maeB | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 630079 | 20 (0.980) | 5 (0.260) | 5/284 | 1.5 | 19.6% | coding (186/2106 nt) | cstA | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| ? | NC_000913 | = 630098 | 22 (1.140) | coding (205/2106 nt) | cstA | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein | |||||
| * | ? | NC_000913 | = 3571080 | 17 (0.840) | 4 (0.210) | 4/278 | 1.7 | 17.8% | coding (240/1974 nt) | glgX | glycogen debranching enzyme |
| ? | NC_000913 | = 3571279 | 21 (1.110) | coding (41/1974 nt) | glgX | glycogen debranching enzyme | |||||
| * | ? | NC_000913 | = 3303996 | 22 (1.080) | 4 (0.210) | 4/276 | 1.7 | 17.6% | coding (549/1008 nt) | yhbW | putative luciferase‑like monooxygenase |
| ? | NC_000913 | = 3304188 | 17 (0.900) | coding (741/1008 nt) | yhbW | putative luciferase‑like monooxygenase | |||||
| * | ? | NC_000913 | = 2713829 | 18 (0.890) | 4 (0.210) | 4/276 | 1.7 | 19.2% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 17 (0.900) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 2713819 = | 18 (0.890) | 4 (0.210) | 4/276 | 1.7 | 19.2% | coding (924/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | 2713920 = | 17 (0.900) | coding (1025/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | = 395765 | 25 (1.230) | 5 (0.260) | 4/280 | 1.7 | 17.4% | coding (523/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase |
| ? | NC_000913 | = 395835 | 24 (1.260) | coding (453/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase | |||||
| * | ? | NC_000913 | = 326558 | 21 (1.030) | 6 (0.320) | 4/278 | 1.7 | 19.8% | coding (690/1671 nt) | betA | choline dehydrogenase, a flavoprotein |
| ? | NC_000913 | = 326641 | 29 (1.530) | coding (607/1671 nt) | betA | choline dehydrogenase, a flavoprotein | |||||
| * | ? | NC_000913 | 3927418 = | 20 (0.980) | 3 (0.160) | 3/274 | 2.0 | 15.6% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 14 (0.750) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | = 285973 | 21 (1.030) | 3 (0.160) | 3/274 | 2.0 | 13.5% | coding (579/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter |
| ? | NC_000913 | = 286392 | 19 (1.020) | coding (998/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter | |||||
| * | ? | NC_000913 | = 3867992 | 23 (1.130) | 3 (0.160) | 3/282 | 2.1 | 11.4% | coding (265/333 nt) | yidQ | DUF1375 family outer membrane protein |
| ? | NC_000913 | = 3868005 | 25 (1.300) | coding (278/333 nt) | yidQ | DUF1375 family outer membrane protein | |||||