mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| MC JC | 575,786 | Δ991 bp | IS5‑mediated | nmpC ← | putative outer membrane porin NmpC |
| JC JC | 577,688 | IS3 (+) +3 bp | coding (76‑78/498 nt) | rrrD → | lysozyme |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,301,917 | C→T | Q246* (CAG→TAG) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,889,802 | G→T | intergenic (‑56/+149) | fadD ← / ← yeaY | long‑chain‑fatty‑acid‑‑CoA ligase/Slp family lipoprotein YeaY |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| MC JC | 2,102,944 | Δ685 bp | IS5‑mediated | [wbbL]–[wbbK] | [wbbL], [wbbK] |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,707,484 | +GA :: IS3 (+) +4 bp | coding (219‑222/1608 nt) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| JC JC | 3,720,136 | IS3 (–) +3 bp | coding (88‑90/213 nt) | cspA → | cold shock protein CspA |
| JC JC | 3,890,411 | IS1 (–) +9 bp | coding (176‑184/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| JC JC | 4,163,521 | IS2 (–) +5 bp | intergenic (‑251/‑114) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase/cobalamin outer membrane transporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 123 [0] | [0] 176 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424463–3424238 | 5–698 | 33 [31] | [32] 33 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 122 (1.260) | 73/598 | 0.1 | 47.7% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 800505 | 134 (1.380) | coding (71/954 nt) | ybhD | putative DNA‑binding transcriptional regulator YbhD | |||||
| * | ? | NC_000913 | = 566774 | 94 (0.970) | 81 (0.840) | 31/594 | 2.2 | 44.8% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 106 (1.100) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 689045 | NA (NA) | 83 (0.860) | 56/598 | 0.5 | 38.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 720172 = | 131 (1.350) | coding (289/2199 nt) | speF | inducible ornithine decarboxylase | |||||
| * | ? | NC_000913 | 1207790 = | 24 (0.250) | 66 (0.720) | 48/566 | 0.7 | 72.6% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 27 (0.290) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.250) | 66 (0.720) | 46/566 | 0.8 | 72.6% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 27 (0.290) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 147 (1.540) | 93/590 | 0.0 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 123 (1.270) | 74/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 58 (0.600) | 36/594 | 1.7 | 40.8% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1995730 | 84 (0.870) | coding (76/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 56 (0.580) | 38/598 | 1.5 | 39.7% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1995729 = | 85 (0.880) | coding (75/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 35 (0.360) | 30/594 | 2.3 | 21.1% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1995543 = | 131 (1.360) | intergenic (‑184/‑112) | uvrY/yecU | DNA‑binding transcriptional activator UvrY/protein YecU | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 176 (1.810) | 106/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | = 1995547 | 128 (1.320) | 34 (0.350) | 28/598 | 2.6 | 21.0% | intergenic (‑188/‑108) | uvrY/yecU | DNA‑binding transcriptional activator UvrY/protein YecU |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3978530 = | 36 (0.370) | 64 (0.660) | 49/598 | 0.8 | 64.0% | coding (1006/1080 nt) | wecF | TDP‑N‑acetylfucosamine:lipid II N‑acetylfucosaminyltransferase |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3978531 | 35 (0.360) | 46 (0.480) | 34/594 | 1.9 | 56.8% | coding (1007/1080 nt) | wecF | TDP‑N‑acetylfucosamine:lipid II N‑acetylfucosaminyltransferase |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||