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 |
| RA | 297,212 | C→T | intergenic (‑116/+169) | intF ← / ← yagP | putative phage integrase/putative LysR family substrate binding domain‑containing protein YagP |
| RA | 366,519 | G→A | A331V (GCG→GTG) | lacI ← | DNA‑binding transcriptional repressor LacI |
| JC JC | 371,758 | IS30 (+) +2 bp | coding (520‑521/867 nt) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 | 1,695,565 | C→T | G169G (GGG→GGA) | uidA ← | beta‑glucuronidase |
| RA | 1,699,275 | C→T | intergenic (‑95/‑80) | malI ← / → malX | DNA‑binding transcriptional repressor MalI/PTS enzyme IIBC component MalX |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| MC JC | 3,090,238 | 688 bp→74 bp | [yggI]–[endA] | [yggI], [endA] | |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,331,656 | T→A | R385R (CGT→CGA) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,346,688 | G→A | V213V (GTC→GTT) | fumB ← | fumarase B |
| RA | 4,360,528 | T→C | A469A (GCA→GCG) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,585,480 | G→A | Q428* (CAA→TAA) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,623,743 | C→T | V125V (GTG→GTA) | lplA ← | lipoate‑‑protein ligase A |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 257908–258674 | 258676 | 3–769 | 35 [0] | [0] 2 | insB9–[crl] | insB9,insA9,[crl] |
| * | * | ÷ | NC_000913 | 364356 | 366432 | 2077 | 2 [0] | [1] 3 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913 | 1694762 | 1695484 | 723 | 2 [0] | [0] 2 | uidA | beta‑glucuronidase |
| * | * | ÷ | NC_000913 | 2407430 | 2407517 | 88 | 2 [1] | [1] 2 | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| * | * | ÷ | NC_000913 | 2413015 | 2413096 | 82 | 2 [1] | [1] 2 | yfbV | PF04217 family membrane protein YfbV |
| * | * | ÷ | NC_000913 | 3423903–3424234 | 3424416–3424238 | 5–514 | 2 [0] | [1] 2 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 66532 | 25 (0.680) | 31 (0.950) +27 bp |
30/428 | 0.2 | 66.6% | coding (19/696 nt) | araD | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| ? | NC_000913 | 70073 = | 10 (0.270) | intergenic (‑25/‑314) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC | |||||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 35 (0.990) | 31/466 | 0.2 | 100% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 275508 | 26 (0.710) | 12 (0.340) | 11/462 | 1.1 | 27.6% | coding (184/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter |
| ? | NC_000913 | 372749 = | 38 (1.080) | coding (635/810 nt) | mhpD | 2‑hydroxypentadienoate hydratase | |||||
| * | ? | NC_000913 | 1207790 = | 5 (0.140) | 6 (0.180) | 4/450 | 2.0 | 52.9% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 6 (0.180) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 4 (0.110) | 10 (0.290) | 9/450 | 1.3 | 67.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 6 (0.180) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 19 (0.520) | 18/480 | 0.7 | 73.1% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2406787 | 7 (0.190) | intergenic (‑146/‑774) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 14 (0.380) | 13/480 | 1.0 | 35.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3131469 = | 26 (0.710) | coding (940/1068 nt) | yghQ | putative transport protein YghQ | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 9 (0.250) | 8/480 | 1.5 | 56.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3263159 = | 7 (0.190) | coding (502/1209 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 32 (0.870) | 32/482 | 0.2 | 80.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3263162 | 8 (0.220) | coding (499/1209 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_000913 | 2424516 = | 10 (0.270) | 25 (0.680) | 24/482 | 0.4 | 71.4% | intergenic (‑7/+1) | hisP/hisM | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit/lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisM |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 21 (0.570) | 20/482 | 0.6 | 48.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3807520 = | 22 (0.600) | coding (579/1035 nt) | waaQ | lipopolysaccharide core heptosyltransferase 3 | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 20 (0.550) | 19/482 | 0.6 | 46.5% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3807527 | 23 (0.630) | coding (572/1035 nt) | waaQ | lipopolysaccharide core heptosyltransferase 3 | |||||
| * | ? | NC_000913 | = 4093990 | 13 (0.360) | 24 (0.750) +29 bp |
23/424 | 0.4 | 66.9% | coding (283/825 nt) | rhaD | rhamnulose‑1‑phosphate aldolase |
| ? | NC_000913 | 4097452 = | 14 (0.380) | intergenic (‑4/‑284) | rhaB/rhaS | rhamnulokinase/DNA‑binding transcriptional activator RhaS | |||||
| * | ? | NC_000913 | 4171749 = | 22 (0.600) | 7 (0.200) +GGAATTAATT |
6/462 | 1.7 | 28.3% | noncoding (113/120 nt) | rrfB | 5S ribosomal RNA |
| ? | NC_000913 | = 4171921 | 15 (0.410) | intergenic (+165/‑136) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 4322811 = | 28 (0.770) | 44 (1.280) | 38/452 | 0.1 | 62.3% | intergenic (‑389/+525) | phnF/phnD | putative transcriptional regulator PhnF/phosphonate/phosphate ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 4322802 | 27 (0.790) | intergenic (‑380/+534) | phnF/phnD | putative transcriptional regulator PhnF/phosphonate/phosphate ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 4628620 | 23 (0.630) | 12 (0.330) | 10/478 | 1.2 | 33.9% | intergenic (+73/+235) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| ? | NC_000913 | 4634847 = | 24 (0.660) | coding (464/870 nt) | rob | DNA‑binding transcriptional dual regulator Rob | |||||
| * | ? | NC_000913 | = 4635603 | 15 (0.410) | 14 (0.380) +G |
14/480 | 0.9 | 51.0% | coding (83/474 nt) | creA | PF05981 family protein CreA |
| ? | NC_000913 | 4638790 = | 12 (0.330) | coding (613/1353 nt) | creD | putative inner membrane protein CreD | |||||