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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,765,197 | 0 | G | A | 51.5% | 12.0 / 46.3 | 33 | V1005V (GTG→GTA) | rhsA | rhs element protein RhsA |
| * | NC_000913 | 3,622,678 | 0 | G | A | 45.4% | 98.5 / 210.6 | 163 | A1163T (GCA→ACA) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,622,662 | 0 | C | T | 45.3% | 12.2 / 207.6 | 159 | L1157L (CTC→CTT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,622,659 | 0 | G | C | 45.0% | ‑3.5 / 277.8 | 160 | A1156A (GCG→GCC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 1,635,488 | 0 | T | A | 44.8% | 78.0 / 203.0 | 134 | A120A (GCA→GCT) | ydfN | Qin prophage; putative side tail fiber assembly protein |
| * | NC_000913 | 3,622,701 | 0 | T | C | 40.6% | 137.2 / 175.3 | 143 | Y1170Y (TAT→TAC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 1,428,097 | 0 | A | C | 39.0% | 23.0 / 64.5 | 41 | L210L (CTT→CTG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 650,809 | 0 | T | G | 36.8% | 53.9 / 11.0 | 38 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.9% | 94.8 / 25.1 | 63 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 888,014 | 0 | T | G | 33.3% | 51.1 / 11.4 | 36 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 753,125 | 0 | T | A | 32.6% | 88.6 / 25.0 | 49 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.9% | 107.2 / 58.9 | 72 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.4% | 82.7 / 14.0 | 35 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.0% | 124.0 / 10.0 | 71 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.9% | 64.1 / 22.9 | 42 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 30.5% | 100.3 / 23.0 | 59 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,906,769 | 0 | A | C | 29.8% | 106.0 / 13.0 | 57 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 28.6% | 99.6 / 11.8 | 56 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,442,146 | 0 | A | G | 28.2% | 134.2 / 22.8 | 78 | S11P (TCC→CCC) | msrA | methionine sulfoxide reductase A |
| * | NC_000913 | 3,622,316 | 0 | G | C | 27.7% | 94.9 / 43.2 | 47 | S1042T (AGC→ACC) | rhsB | rhs element protein RhsB |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 85 (1.140) | 15 (0.230) | 14/244 | 3.2 | 17.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 71 (1.080) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 12 (0.210) | 11/216 | 3.4 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 15 (0.290) | 8/190 | 3.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 2375831 | 0 (0.000) | 11 (0.150) | 9/268 | 4.9 | 100% | coding (132/963 nt) | menC | o‑succinylbenzoate synthase |
| ? | NC_000913 | 2514273 = | NA (NA) | noncoding (1/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 9 (0.170) | 4/202 | 5.7 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 4 (0.060) | 4/268 | 6.9 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 7 (0.100) | 4/268 | 6.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 555833 | 79 (1.060) | 3 (0.050) | 3/244 | 7.0 | 4.5% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 58 (0.880) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 4357858 = | 125 (1.680) | 3 (0.040) | 3/258 | 7.3 | 2.5% | coding (760/2148 nt) | cadA | lysine decarboxylase 1 |
| ? | NC_000913 | = 4357854 | 121 (1.740) | coding (764/2148 nt) | cadA | lysine decarboxylase 1 | |||||
| * | ? | NC_000913 | 3953045 = | 75 (1.010) | 4 (0.060) | 3/258 | 7.3 | 5.5% | coding (562/930 nt) | ilvE | branched‑chain‑amino‑acid aminotransferase |
| ? | NC_000913 | 3953125 = | 68 (0.980) | coding (642/930 nt) | ilvE | branched‑chain‑amino‑acid aminotransferase | |||||