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 | 667,643 | T→C | N192S (AAT→AGT) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 684,941 | C→T | V105V (GTG→GTA) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| MC JC | 716,842 | Δ10 bp | intergenic (‑245/+95) | ybfG ← / ← potE | PF10964 domain‑containing protein YbfG/putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 838,498 | T→G | intergenic (‑42/+32) | ybiI ← / ← ybiX | zinc finger domain‑containing protein YbiI/PKHD‑type hydroxylase YbiX |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,102,028 | T→C | N34D (AAC→GAC) | csgF ← | curli assembly component |
| 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 |
| 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 | 2,193,328 | G→A | H281Y (CAT→TAT) | mrp ← | P‑loop NTPase family protein |
| RA | 2,696,638 | +AT | coding (838/1557 nt) | mltF → | membrane‑bound lytic murein transglycosylase F |
| JC | 2,816,330 | (TGTGC)1→2 | coding (110/1557 nt) | gshA ← | glutamate‑‑cysteine ligase |
| JC | 3,277,273 | (TTCAACA)2→3 | coding (272/336 nt) | prlF → | antitoxin PrlF |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,371,175 | A→T | L467* (TTG→TAG) | nanT ← | N‑acetylneuraminate:H(+) symporter |
| RA | 3,428,558 | T→C | noncoding (205/1542 nt) | rrsD ← | 16S ribosomal RNA |
| 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 | 4,296,381 | +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 | 1096995 | 1097569 | 575 | 51 [1] | [15] 16 | [serX] | [serX] |
| * | * | ÷ | NC_000913 | 1196257 | 1211438 | 15182 | 17 [15] | [15] 18 | [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 | 1552114–1552186 | 1552271–1552213 | 28–158 | 17 [13] | [15] 16 | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424552–3424239 | 7–783 | 19 [15] | [15] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4035266–4035733 | 4036975–4035735 | 3–1710 | 16 [15] | [14] 17 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 925857 = | 39 (0.670) | 17 (0.440) | 8/184 | 2.8 | 56.8% | intergenic (+317/+27) | clpA/serW | ATP‑dependent Clp protease ATP‑binding subunit ClpA/tRNA‑Ser |
| ? | NC_000913 | = 1096994 | 0 (0.000) | intergenic (+165/+571) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 54 (0.960) | 37/268 | 0.4 | 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 | 3363001 = | 70 (1.200) | 97 (1.680) | 55/274 | 0.1 | 73.4% | 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) | 61 (1.050) | 39/276 | 0.4 | 98.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 28 (0.480) | 14 (0.260) | 14/258 | 2.5 | 28.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 43 (0.790) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||