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 | freq | annotation | gene | description |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 710,595 | G→T | 100% | P18T (CCT→ACT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 940,751 | T→C | 10.1% | intergenic (+31/‑208) | serS → / → dmsA | serine‑‑tRNA ligase/dimethyl sulfoxide reductase subunit A |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,028,160 | G→C | 16.4% | intergenic (‑143/+28) | dgcQ ← / ← yodC | putative diguanylate cyclase DgcQ/protein YodC |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,402,140 | G→A | 100% | P569L (CCG→CTG) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,657,599 | T→A | 9.6% | intergenic (+32/+387) | hdeD → / ← arrS | acid‑resistance membrane protein/small regulatory RNA ArrS |
| RA | 3,657,601 | G→C | 10.0% | intergenic (+34/+385) | hdeD → / ← arrS | acid‑resistance membrane protein/small regulatory RNA ArrS |
| RA | 3,657,603 | T→A | 10.1% | intergenic (+36/+383) | hdeD → / ← arrS | acid‑resistance membrane protein/small regulatory RNA ArrS |
| RA | 3,719,704 | C→T | 8.3% | A76V (GCC→GTC) | yiaG → | putative DNA‑binding transcriptional regulator YiaG |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,125,097 | C→T | 100% | E572K (GAG→AAG) | priA ← | primosome factor N' |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 17.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | 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 | 1196276 | 1211449 | 15174 | 9 [8] | [7] 9 | [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] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 213083 = | 39 (1.180) | 3 (0.090) | 3/256 | NT | 7.6% | coding (753/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase |
| ? | NC_000913 | 213120 = | 35 (1.090) | coding (790/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 4 (0.130) | 4/250 | NT | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 392264 = | NA (NA) | 6 (0.190) | 4/256 | NT | NA | noncoding (703/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392281 = | NA (NA) | noncoding (686/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2185 (66.390) | 260/262 | NT | 98.7% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 28 (0.840) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 1409894 = | 27 (0.810) | 3 (0.090) | 3/252 | NT | 11.0% | coding (384/1374 nt) | dbpA | ATP‑dependent RNA helicase DbpA |
| ? | NC_000913 | 1409908 = | 23 (0.730) | coding (398/1374 nt) | dbpA | ATP‑dependent RNA helicase DbpA | |||||
| * | ? | NC_000913 | = 1999548 | 18 (0.540) | 4 (0.130) | 4/248 | NT | 18.2% | intergenic (‑68/+37) | dcyD/tcyJ | D‑cysteine desulfhydrase/cystine ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1999563 | 19 (0.610) | intergenic (‑83/+22) | dcyD/tcyJ | D‑cysteine desulfhydrase/cystine ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3600976 = | 36 (1.090) | 3 (0.100) | 3/240 | NT | 8.5% | intergenic (‑193/+52) | rpoH/ftsX | RNA polymerase, sigma 32 (sigma H) factor/cell division protein FtsX |
| ? | NC_000913 | 3601013 = | 32 (1.060) | intergenic (‑230/+15) | rpoH/ftsX | RNA polymerase, sigma 32 (sigma H) factor/cell division protein FtsX | |||||
| * | ? | NC_000913 | = 4285380 | NA (NA) | 3 (0.160) +56 bp |
3/152 | NT | NA | intergenic (‑167/+33) | yjcH/acs | conserved inner membrane protein YjcH/acetyl‑CoA synthetase (AMP‑forming) |
| ? | NC_000913 | = 4460444 | NA (NA) | noncoding (29/36 nt) | other | REP338a | |||||
| * | ? | NC_000913 | 4365125 = | 40 (1.210) | 3 (0.100) | 3/250 | NT | 7.4% | coding (232/339 nt) | cutA | copper binding protein CutA |
| ? | NC_000913 | 4365142 = | 37 (1.180) | coding (215/339 nt) | cutA | copper binding protein CutA | |||||