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 |
| RA | 224,846 | T→C | noncoding (1076/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,851 | A→G | noncoding (1081/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,885 | T→C | noncoding (1115/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,889 | C→T | noncoding (1119/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,893 | T→A | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,903 | 2 bp→AC | noncoding (1133‑1134/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,906 | C→T | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,910 | 2 bp→GT | noncoding (1140‑1141/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,915 | A→C | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,920 | A→T | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,923 | G→A | noncoding (1153/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,933 | A→G | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,938 | T→C | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,943 | T→C | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,968 | G→A | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,977 | G→C | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 225,499 | T→A | intergenic (+42/‑1) | ileV → / → alaV | tRNA‑Ile/tRNA‑Ala |
| RA | 225,505 | T→C | noncoding (6/76 nt) | alaV → | tRNA‑Ala |
| RA | 225,531 | T→C | noncoding (32/76 nt) | alaV → | tRNA‑Ala |
| RA | 225,537 | C→A | noncoding (38/76 nt) | alaV → | tRNA‑Ala |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 435,813 | T→A | D60E (GAT→GAA) | thiL → | thiamine monophosphate kinase |
| RA | 571,663 | T→C | Y70Y (TAT→TAC) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 583,505 | A→T | intergenic (+445/‑176) | tfaX → / → appY | DLP12 prophage; protein TfaX/DNA‑binding transcriptional activator AppY |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,052,605 | T→G | D253A (GAC→GCC) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,622,811 | A→G | intergenic (+70/+6) | mgtS → / ← mgrR | small protein MgtS/small regulatory RNA MgrR |
| 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 | 2,406,063 | Δ1 bp | coding (579/939 nt) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,490,314 | G→A | A546V (GCA→GTA) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,494,424 | T→C | intergenic (‑22/‑274) | yfdX ← / → ypdI | protein YfdX/colanic acid synthesis putative lipoprotein YpdI |
| RA | 2,626,944 | C→T | L665L (CTG→CTA) | pdeF ← | cyclic di‑GMP phosphodiesterase PdeF |
| 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 | 4,037,198 | A→G | noncoding (58/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,037,207 | C→A | noncoding (67/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,037,213 | T→C | noncoding (73/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,039,467 | G→A | noncoding (1949/2905 nt) | rrlA → | 23S ribosomal RNA |
| 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 | 1196286 | 1211433 | 15148 | 7 [6] | [6] 7 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423787–3424523 | 3424523 | 1–737 | 7 [6] | [4] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225496 = | 7 (0.170) | 25 (0.760) +26 bp |
11/224 | 1.4 | 86.1% | intergenic (+39/‑4) | ileV/alaV | tRNA‑Ile/tRNA‑Ala |
| ? | NC_000913 | = 4037217 | 3 (0.070) | noncoding (77/77 nt) | ileT | tRNA‑Ile | |||||
| * | ? | NC_000913 | 225500 = | 8 (0.200) | 44 (1.380) +30 bp |
16/216 | 0.7 | 91.1% | noncoding (1/76 nt) | alaV | tRNA‑Ala |
| ? | NC_000913 | = 4037217 | 3 (0.070) | noncoding (77/77 nt) | ileT | tRNA‑Ile | |||||
| * | ? | NC_000913 | = 781143 | 52 (1.280) | 11 (0.300) +TAAACACTTTTTAAC |
7/246 | 2.4 | 28.2% | noncoding (76/76 nt) | valZ | tRNA‑Val |
| ? | NC_000913 | 2947605 = | 11 (0.270) | intergenic (+32/‑2) | metW/metV | tRNA‑Met/tRNA‑Met | |||||
| * | ? | NC_000913 | 3363001 = | 52 (1.280) | 59 (1.460) | 38/274 | 0.1 | 68.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.070) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 34 (0.830) | 26/276 | 0.4 | 89.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.100) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 22 (0.540) | 18 (0.470) | 16/258 | 1.1 | 46.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 21 (0.550) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 22 (0.540) | 10 (0.260) | 10/258 | 1.9 | 32.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 21 (0.550) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||