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 | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 905,528 | G→T | G206W (GGG→TGG) | amiD → | N‑acetylmuramoyl‑L‑alanine amidase D |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 | 2,630,593 | G→T | E90* (GAA→TAA) | yfgI → | nalidixic acid resistance protein YfgI |
| 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 | 4,140,748 | C→A | A492S (GCC→TCC) | ptsA ← | putative PTS multiphosphoryl transfer protein PtsA |
| 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 |
| RA | 4,505,167 | C→A | G370G (GGC→GGA) | yjhB → | putative sialic acid transporter |
| RA | 4,568,243 | C→A | A93S (GCC→TCC) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102986 | 3104066 | 1081 | 7 [6] | [6] 7 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423785–3424233 | 3424525–3424240 | 8–741 | 9 [5] | [5] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 339959 = | NA (NA) | 7 (0.240) +28 bp |
7/220 | 2.0 | NA | coding (167/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377433 = | NA (NA) | intergenic (+122/+102) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 57 (2.300) | 14/190 | 0.6 | 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 | = 374963 | NA (NA) | 66 (2.660) | 23/190 | 0.1 | 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 | 375001 = | NA (NA) | 12 (0.420) | 5/216 | 2.5 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 8 (0.220) +T |
8/274 | 2.3 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 16 (0.640) | 9/192 | 1.3 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 24 (0.850) | 15/216 | 0.7 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 12 (0.480) | 4/192 | 2.6 | 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) | 14 (0.390) +T |
9/274 | 2.1 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 46 (1.630) | 25/216 | 0.2 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 5 (0.160) | 5/238 | 2.8 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 377353 = | NA (NA) | 12 (0.420) +30 bp |
7/216 | 2.0 | NA | noncoding (18/37 nt) | other | REP32a |
| ? | NC_000913 | 4325850 = | NA (NA) | intergenic (‑109/+549) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 12 (0.410) | 5/224 | 2.6 | 33.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 24 (0.820) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 699424 = | NA (NA) | 6 (0.220) | 4/206 | 2.7 | NA | intergenic (‑247/+150) | asnB/umpH | asparagine synthetase B/UMP phosphatase |
| ? | NC_000913 | = 2133430 | NA (NA) | intergenic (‑33/+60) | wcaA/wzc | putative colanic acid biosynthesis glycosyl transferase/protein‑tyrosine kinase Wzc | |||||
| * | ? | NC_000913 | = 1134685 | NA (NA) | 4 (0.150) | 4/204 | 2.7 | NA | intergenic (+128/‑44) | flgF/flgG | flagellar basal‑body rod protein FlgF/flagellar basal‑body rod protein FlgG |
| ? | NC_000913 | = 4326248 | NA (NA) | intergenic (‑507/+151) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | 1207790 = | 11 (0.300) | 32 (1.000) | 27/244 | 0.2 | 78.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 8 (0.250) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.300) | 26 (0.810) | 18/244 | 0.7 | 74.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 8 (0.250) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 2304714 = | NA (NA) | 6 (0.190) +GCAAGCGTCGCATCAGGCA |
5/238 | 2.8 | NA | noncoding (17/36 nt) | other | REP161f |
| ? | NC_000913 | = 4296059 | NA (NA) | intergenic (+265/+377) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | 2518092 = | 34 (0.940) | 8 (0.250) | 7/240 | 2.2 | 20.1% | noncoding (25/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2521076 = | 34 (1.080) | noncoding (26/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | 3045988 = | 33 (0.910) | 35 (1.040) | 7/256 | 2.4 | 59.5% | intergenic (‑87/+180) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| ? | NC_000913 | 3046089 = | 17 (0.510) | intergenic (‑188/+79) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase | |||||
| * | ? | NC_000913 | = 3281704 | NA (NA) | 15 (0.440) | 8/262 | 2.2 | NA | noncoding (2/36 nt) | other | REP239a |
| ? | NC_000913 | = 3281780 | NA (NA) | noncoding (5/34 nt) | other | REP239b | |||||
| * | ? | NC_000913 | 3363001 = | 46 (1.270) | 70 (1.950) | 42/274 | 0.0 | 75.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 46 (1.270) | 33/276 | 0.1 | 92.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.110) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 15 (0.450) | 9/256 | 1.9 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||