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 | 67,483 | C→T | L285L (CTG→CTA) | araA ← | L‑arabinose isomerase |
| RA | 82,372 | T→C | E386E (GAA→GAG) | leuA ← | 2‑isopropylmalate synthase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 367,852 | (GC)6→5 | coding (568‑569/834 nt) | mhpR ← | mhp operon transcriptional activator |
| RA | 757,037 | T→C | D377D (GAT→GAC) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 809,038 | C→T | A74T (GCC→ACC) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 940,856 | A→G | intergenic (+136/‑103) | serS → / → dmsA | seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A |
| 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 | 1,349,856 | T→C | E84E (GAA→GAG) | yciW ← | putative oxidoreductase |
| RA | 1,426,023 | A→G | pseudogene (394/453 nt) | ydaY → | pseudogene, Rac prophage;Phage or Prophage Related |
| RA | 1,488,624 | T→C | R131R (CGT→CGC) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,500,389 | (T)8→7 | coding (61/981 nt) | ydcK ← | uncharacterized protein |
| RA | 1,785,500 | +T | coding (1613/2379 nt) | ppsA ← | phosphoenolpyruvate synthase |
| 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 | 2,096,825 | T→C | F71S (TTC→TCC) | hisI → | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase |
| 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 | 2,524,685 | T→A | H65L (CAT→CTT) | xapA ← | purine nucleoside phosphorylase 2; nicotinamide 1‑beta‑D‑riboside synthase |
| RA | 2,619,803 | A→G | F120L (TTT→CTT) | uraA ← | uracil permease |
| RA | 2,673,499 | C→T | P52S (CCA→TCA) | yphA → | DoxX family inner membrane protein |
| JC JC | 2,805,832 | IS1 (–) +9 bp | coding (1018‑1026/1203 nt) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,850,439 | C→T | intergenic (‑4/‑208) | hycA ← / → hypA | regulator of the transcriptional regulator FhlA/protein involved in nickel insertion into hydrogenases 3 |
| JC | 2,859,224 | (GGCGTG)2→3 | coding (2132/2562 nt) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,860,556 | G→A | Q227* (CAG→TAG) | ygbI ← | DeoR family putative transcriptional regulator |
| RA | 3,016,617 | G→A | L186L (CTG→CTA) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,174,815 | C→T | L194L (TTG→TTA) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,226,782 | C→T | D183D (GAC→GAT) | ygjI → | putative transporter |
| RA | 3,235,823 | G→A | A18V (GCG→GTG) | rlmG ← | 23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,271,629 | T→C | T48A (ACG→GCG) | garK ← | glycerate kinase I |
| RA | 3,291,373 | G→A | L11L (TTG→TTA) | yraK → | putative fimbrial‑like adhesin protein |
| 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 | 3,576,956 | A→G | S36P (TCC→CCC) | gntU ← | gluconate transporter, low affinity GNT 1 system |
| RA | 3,624,042 | (G)6→7 | pseudogene (156/351 nt) | yrhC → | pseudogene fragment |
| 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 | 3,922,549 | (C)5→6 | intergenic (‑109/+508) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| 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 | 3,990,828 | G→A | intergenic (‑62/‑325) | hemC ← / → cyaA | hydroxymethylbilane synthase/adenylate cyclase |
| RA | 4,086,147 | G→A | A44A (GCG→GCA) | fdhD → | formate dehydrogenase formation protein |
| 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 | 3423723–3424581 | 3424581 | 1–859 | 48 [46] | [47] 48 | [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) | 100 (1.150) | 87/290 | 0.0 | 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 | |||||