mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 82,372 | T→C | E386E (GAA→GAG) | leuA ← | 2‑isopropylmalate synthase |
| RA | 146,566 | G→A | A43A (GCC→GCT) | panD ← | aspartate 1‑decarboxylase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 569,541 | Δ1 bp | coding (640/1527 nt) | ybcK → | DLP12 prophage; putative recombinase |
| RA | 656,251 | C→T | intergenic (‑283/‑306) | dcuC ← / → pagP | anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase |
| RA | 809,038 | C→T | A74T (GCC→ACC) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 962,923 | A→G | D310G (GAC→GGC) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,198,201 | C→T | E13K (GAA→AAA) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,238,213 | G→C | G215R (GGG→CGG) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,349,856 | T→C | E84E (GAA→GAG) | yciW ← | putative oxidoreductase |
| RA | 1,474,862 | C→G | G214G (GGC→GGG) | ydbC → | putative NAD(P)‑binding oxidoreductase |
| RA | 1,488,624 | T→C | R131R (CGT→CGC) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,594,132 | (C)8→9 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,641,252 | T→C | intergenic (‑667/+87) | essQ ← / ← cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| RA | 1,643,723 | T→C | K194K (AAA→AAG) | ydfU ← | Qin prophage; uncharacterized protein |
| RA | 1,671,752 | A→G | intergenic (+68/‑25) | asr → / → ydgU | acid shock‑inducible periplasmic protein/stationary phase‑induced protein |
| RA | 1,719,444 | C→T | Q53Q (CAG→CAA) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,729,289 | G→A | R68Q (CGG→CAG) | lhr → | putative ATP‑dependent helicase |
| RA | 1,817,424 | A→G | C359C (TGT→TGC) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| RA | 1,842,587 | C→T | Q73* (CAG→TAG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,953,212 | G→A | A171T (GCC→ACC) | cmoA → | carboxy‑SAM synthase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,181,988 | G→A | W298* (TGG→TAG) | yegV → | putative kinase |
| RA | 2,369,371 | G→A | D445N (GAT→AAT) | arnA → | fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase |
| RA | 2,509,609 | A→C | intergenic (‑183/‑21) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,619,803 | A→G | F120L (TTT→CTT) | uraA ← | uracil permease |
| JC JC | 2,805,832 | IS1 (–) +9 bp | coding (1018‑1026/1203 nt) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| JC | 2,859,224 | (GGCGTG)2→3 | coding (2132/2562 nt) | mutS → | methyl‑directed mismatch repair protein |
| RA | 3,016,617 | G→A | L186L (CTG→CTA) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,214,148 | G→A | G368S (GGT→AGT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,291,373 | G→A | L11L (TTG→TTA) | yraK → | putative fimbrial‑like adhesin protein |
| RA | 3,436,622 | T→C | R35R (CGT→CGC) | trkA → | NAD‑binding component of TrK potassium transporter |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,584,367 | C→T | intergenic (+58/‑392) | yrhA → / → yrhB | pseudogene, interrupted by IS1E/stable heat shock chaperone |
| RA | 3,677,182 | (T)6→7 | coding (1169/2061 nt) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,736,471 | A→G | V236A (GTG→GCG) | bax ← | putative glucosaminidase |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,823,861 | C→T | R488C (CGT→TGT) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,901,405 | C→T | L272L (CTG→CTA) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,923,204 | G→A | G159G (GGC→GGT) | rsmG ← | 16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| RA | 3,951,681 | T→C | pseudogene (140/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,970,392 | C→T | P87L (CCA→CTA) | wecB → | UDP‑N‑acetyl glucosamine‑2‑epimerase |
| RA | 4,086,147 | G→A | A44A (GCG→GCA) | fdhD → | formate dehydrogenase formation protein |
| RA | 4,181,706 | C→T | G154G (GGC→GGT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,185,708 | T→C | L120P (CTG→CCG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,410,605 | C→T | A18V (GCG→GTG) | yjfJ → | PspA/IM30 family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423716–3424234 | 3424585–3424238 | 5–870 | 41 [39] | [40] 41 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 80 (1.060) | 67/290 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||