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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 391,716 | A→C | intergenic (+8/+23) | yaiT → / ← insF‑2 | putative autotransporter YaiT/IS3 element protein InsF |
| RA | 747,140 | C→A | P210P (CCG→CCT) | abrB ← | putative regulator |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,255,245 | G→T | intergenic (‑59/‑110) | rihB ← / → yeiL | pyrimidine‑specific ribonucleoside hydrolase RihB/putative DNA‑binding transcriptional regulator YeiL |
| RA | 2,366,690 | C→A | H261N (CAC→AAC) | arnB → | UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| RA | 3,036,345 | C→A | intergenic (‑63/+28) | prfB ← / ← recJ | peptide chain release factor RF2/ssDNA‑specific exonuclease RecJ |
| RA | 3,074,162 | T→G | A176A (GCA→GCC) | yggC ← | P‑loop NTPase domain‑containing protein YggC |
| RA | 3,172,601 | G→T | L24L (CTG→CTT) | mdaB → | NADPH:quinone oxidoreductase MdaB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| 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 | 3102926 | 3104067 | 1142 | 9 [8] | [8] 10 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423782–3424233 | 3424530–3424238 | 6–749 | 9 [7] | [8] 9 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 60 (2.130) | 22/190 | 0.2 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 23 (0.770) | 7/202 | 2.1 | 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 | = 374963 | NA (NA) | 49 (1.740) | 20/190 | 0.3 | 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 | 375023 = | NA (NA) | 9 (0.320) | 5/192 | 2.6 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 30 (0.740) +T |
15/274 | 1.4 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 46 (1.300) | 22/238 | 0.5 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 56 (1.750) | 18/216 | 0.6 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 22 (0.770) | 6/192 | 2.3 | NA | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 26 (0.640) +T |
12/274 | 1.9 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 22 (0.620) | 11/238 | 1.7 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 59 (1.840) | 29/216 | 0.1 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 9 (0.250) +GAACGCCTTATCCGGT |
7/244 | 2.6 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 25 (0.750) | 10/224 | 1.7 | 47.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 28 (0.840) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.850) | 7 (0.190) | 7/244 | 2.6 | 20.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 22 (0.610) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.850) | 8 (0.220) | 7/244 | 2.6 | 23.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 22 (0.610) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 62 (1.560) | 47/268 | 0.0 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2514272 | 21 (0.630) | 11 (0.330) | 9/224 | 1.9 | 34.4% | intergenic (+28/‑59) | nupC/insL‑3 | nucleoside:H(+) symporter NupC/putative IS186/IS421 transposase |
| ? | NC_000913 | = 2515617 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 3045988 = | 19 (0.460) | 34 (0.900) | 10/256 | 2.1 | 63.2% | intergenic (‑87/+180) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| ? | NC_000913 | 3046089 = | 22 (0.580) | intergenic (‑188/+79) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase | |||||
| * | ? | NC_000913 | 3363001 = | 66 (1.610) | 80 (1.970) | 53/274 | 0.0 | 70.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 46 (1.120) | 39/276 | 0.1 | 97.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 26 (0.780) | 10/226 | 1.8 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 37 (0.970) | 12/256 | 1.7 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | = 4628780 | NA (NA) | 9 (0.250) | 6/240 | 2.9 | NA | noncoding (37/37 nt) | other | REP354b |
| ? | NC_000913 | = 4633089 | NA (NA) | intergenic (+3/+144) | trpR/yjjX | DNA‑binding transcriptional repressor TrpR/ITPase/XTPase | |||||