mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 178,854 | C→A | A100A (GCG→GCT) | mtn ← | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase |
| RA | 184,827 | A→T | D81E (GAT→GAA) | yaeI ← | phosphodiesterase YaeI |
| RA | 231,075 | C→A | intergenic (‑194/‑47) | yafC ← / → yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 299,095 | C→A | G614* (GGA→TGA) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 358,273 | C→A | E140* (GAG→TAG) | cynR ← | DNA‑binding transcriptional dual regulator CynR |
| RA | 453,631 | C→A | Q179H (CAG→CAT) | yajG ← | putative lipoprotein YajG |
| RA | 676,177 | T→A | Q124L (CAG→CTG) | ybeQ ← | Sel1 repeat‑containing protein YbeQ |
| RA | 783,577 | G→T | A138S (GCA→TCA) | pnuC → | nicotinamide riboside transporter |
| RA | 794,131 | G→T | L172M (CTG→ATG) | modE ← | DNA‑binding transcriptional dual regulator ModE |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 956,238 | G→A | P132L (CCG→CTG) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 996,639 | G→T | G102G (GGC→GGA) | ssuA ← | aliphatic sulfonate ABC transporter periplasmic binding protein |
| RA | 1,029,456 | C→A | G172C (GGC→TGC) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,050,314 | G→T | V96V (GTG→GTT) | insB‑4 → | IS1 protein InsB |
| RA | 1,101,296 | G→T | S130Y (TCT→TAT) | csgG ← | curli secretion channel |
| RA | 1,110,743 | G→T | G470V (GGC→GTC) | opgG → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
| RA | 1,124,441 | C→A | G296C (GGC→TGC) | mdtH ← | multidrug efflux pump MdtH |
| RA | 1,144,145 | G→T | R75S (CGC→AGC) | rne ← | ribonuclease E |
| RA | 1,165,787 | G→T | intergenic (+102/‑298) | ycfP → / → ndh | UPF0227 protein YcfP/NADH:quinone oxidoreductase II |
| RA | 1,179,213 | G→T | Q207H (CAG→CAT) | nagK → | N‑acetyl‑D‑glucosamine kinase |
| RA | 1,220,830 | G→T | pseudogene (1230/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,493,756 | C→T | I429I (ATC→ATT) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,595,279 | C→A | pseudogene (2808/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,600,162 | C→A | A16A (GCG→GCT) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,602,280 | C→G | A264G (GCC→GGC) | lsrA → | Autoinducer‑2 ABC transporter ATP binding subunit |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,774,671 | C→G | intergenic (+16/‑15) | ydiB → / → aroD | shikimate dehydrogenase/quinate dehydrogenase/3‑dehydroquinate dehydratase |
| RA | 1,838,849 | C→T | P35S (CCG→TCG) | ynjD → | putative ABC transporter ATP‑binding protein YnjD |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,922,705 | C→A | A89S (GCA→TCA) | pphA ← | phosphoprotein phosphatase 1 |
| RA | 1,933,781 | C→A | W275L (TGG→TTG) | edd ← | phosphogluconate dehydratase |
| 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 | 2,311,895 | C→A | Q285H (CAG→CAT) | ompC ← | outer membrane porin C |
| RA | 2,362,947 | T→C | Q229Q (CAA→CAG) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,366,037 | C→A | A43E (GCG→GAG) | arnB → | UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| RA | 2,524,558 | C→A | L107L (CTG→CTT) | xapA ← | xanthosine phosphorylase |
| RA | 2,581,450 | G→T | A605A (GCG→GCT) | tktB → | transketolase 2 |
| RA | 2,635,100 | C→A | A290D (GCC→GAC) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,762,828 | C→T | S238N (AGC→AAC) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,870,961 | G→T | A115E (GCG→GAG) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,884,319 | T→C | intergenic (‑181/+234) | casA ← / ← cas3 | type I‑E CRISPR system Cascade subunit CasA/CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 2,886,423 | C→A | R266L (CGG→CTG) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 3,097,705 | C→A | R147S (CGC→AGC) | yggW → | putative coproporphyrinogen‑III oxidase‑like protein YggW |
| RA | 3,229,438 | C→A | P184H (CCT→CAT) | ygjK → | glycoside hydrolase |
| RA | 3,257,661 | G→C | A117G (GCG→GGG) | cyuP ← | putative D/L‑serine transporter |
| RA | 3,288,595 | C→A | P169Q (CCA→CAA) | yraI → | putative fimbrial chaperone YraI |
| RA | 3,352,782 | C→A | E82* (GAG→TAG) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,431,335 | C→A | T27T (ACG→ACT) | tsaC ← | threonylcarbamoyl‑AMP synthase |
| RA | 3,498,512 | G→T | G229W (GGG→TGG) | cysG → | siroheme synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,605,651 | G→T | intergenic (‑41/‑100) | yhhM ← / → yhhN | DUF2500 domain‑containing protein YhhM/conserved inner membrane enzyme YhhN |
| RA | 3,715,785 | C→A | G204W (GGG→TGG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,816,706 | C→A | R11S (CGT→AGT) | yicC → | UPF0701 family protein YicC |
| RA | 3,871,793 | G→T | intergenic (‑63/+57) | dgoT ← / ← dgoD | putative D‑galactonate transporter/D‑galactonate dehydratase |
| RA | 3,872,281 | G→T | R240S (CGC→AGC) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,888,391 | G→T | intergenic (+199/‑44) | mnmE → / → tnaC | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit/tnaAB operon leader peptide |
| RA | 3,929,273 | G→A | R111* (CGA→TGA) | viaA ← | protein ViaA |
| RA | 4,032,189 | G→A | L343L (CTG→CTA) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,213,186 | G→T | intergenic (+27/‑48) | rrfE → / → yjaA | 5S ribosomal RNA/stress response protein |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,278,951 | C→A | A158D (GCT→GAT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,335,878 | G→T | P385Q (CCG→CAG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,393,493 | C→A | G192V (GGA→GTA) | queG ← | epoxyqueuosine reductase |
| RA | 4,494,056 | C→A | M117I (ATG→ATT) | idnD ← | L‑idonate 5‑dehydrogenase |
| RA | 4,636,928 | C→A | P78Q (CCG→CAG) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1640924 | 1641100 | 177 | 58 [52] | [50] 59 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock‑like protein CspB |
| * | * | ÷ | NC_000913 | 2033803 | 2033971 | 169 | 55 [48] | [53] 55 | rseX/yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 3102949 | 3104091 | 1143 | 56 [53] | [51] 55 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423761–3424234 | 3426760–3424653 | 420–3000 | 54 [52] | [51] 54 | [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) | 110 (0.760) | 68/270 | 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 = | 184 (1.230) | 191 (1.290) | 89/276 | 0.1 | 67.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 178 (1.190) | 85/278 | 0.1 | 97.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||