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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 436,419 | T→C | G262G (GGT→GGC) | thiL → | thiamine monophosphate kinase |
| RA | 809,038 | C→T | A74T (GCC→ACC) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 815,771 | C→T | A293T (GCG→ACG) | ybhK ← | putative CofD superfamily transferase |
| RA | 927,371 | C→T | R21H (CGT→CAT) | aat ← | leucyl/phenylalanyl‑tRNA‑protein transferase |
| RA | 962,923 | A→G | D310G (GAC→GGC) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,027,735 | A→G | C13C (TGT→TGC) | yccT ← | UPF0319 family protein |
| RA | 1,198,201 | C→T | E13K (GAA→AAA) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,219,569 | G→A | intergenic (+368/‑32) | ymgF → / → ycgH | inner membrane division septum protein/pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,349,856 | T→C | E84E (GAA→GAG) | yciW ← | putative oxidoreductase |
| RA | 1,363,075 | A→G | K111K (AAA→AAG) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase |
| RA | 1,488,624 | T→C | R131R (CGT→CGC) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,704,875 | G→A | intergenic (+199/‑74) | blr → / → cnu | beta‑lactam resistance membrane protein; divisome‑associated protein/nucleoid‑associated oriC‑binding protein; H‑NS and StpA stabilizing factor |
| RA | 1,785,280 | G→A | G611G (GGC→GGT) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,912,482 | Δ2 bp | coding (94‑95/882 nt) | htpX ← | putative endopeptidase |
| 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 | 1,987,693 | G→A | I22I (ATC→ATT) | yecJ ← | DUF2766 family protein |
| 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 | 2,231,778 | G→T | intergenic (+64/‑66) | yohK → / → cdd | LrgB family inner membrane protein/cytidine/deoxycytidine deaminase |
| RA | 2,369,371 | G→A | D445N (GAT→AAT) | arnA → | fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase |
| RA | 2,421,749 | C→T | R14R (CGC→CGT) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,493,798 | A→G | I202T (ATC→ACC) | yfdX ← | uncharacterized protein |
| RA | 2,619,803 | A→G | F120L (TTT→CTT) | uraA ← | uracil permease |
| RA | 2,682,157 | (C)7→8 | coding (589/3282 nt) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| JC JC | 2,805,832 | IS1 (–) +9 bp | coding (1018‑1026/1203 nt) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,839,302 | T→C | intergenic (‑38/‑222) | ascG ← / → ascF | asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components |
| RA | 2,843,150 | G→A | A99A (GCC→GCT) | hycH ← | hydrogenase 3 maturation protein |
| RA | 2,843,719 | C→T | E164E (GAG→GAA) | hycG ← | hydrogenase 3 and formate hydrogenase complex, HycG subunit |
| JC | 2,859,224 | (GGCGTG)2→3 | coding (2132/2562 nt) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,926,997 | C→T | N230N (AAC→AAT) | ygdH → | UPF0717 family protein |
| RA | 2,965,974 | C→T | A22T (GCG→ACG) | lgt ← | phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase |
| RA | 3,016,617 | G→A | L186L (CTG→CTA) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,057,347 | T→C | N355S (AAC→AGC) | serA ← | D‑3‑phosphoglycerate dehydrogenase |
| 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 | 3,708,380 | C→T | intergenic (‑675/+236) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| 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 | 3,826,728 | A→G | T507A (ACC→GCC) | recG → | ATP‑dependent DNA helicase |
| 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 | 4,185,708 | 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 |
| RA | 4,549,509 | G→A | A234A (GCG→GCA) | fimH → | minor component of type 1 fimbriae |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423743–3424234 | 3424582–3424238 | 5–840 | 42 [41] | [41] 42 | [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) | 78 (1.000) | 70/290 | 0.1 | 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 | |||||