mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 200,396 | G→T | intergenic (+36/‑86) | bamA → / → skp | outer membrane protein assembly factor BamA/periplasmic chaperone Skp |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 339,935 | C→T | A56V (GCC→GTC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,941 | C→T | T58I (ACT→ATT) | yahH → | putative uncharacterized protein YahH |
| RA | 339,958 | G→A | D64N (GAC→AAC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,986 | G→A | R73Q (CGA→CAA) | yahH → | putative uncharacterized protein YahH |
| RA | 362,541 | T→A | A213A (GCA→GCT) | lacY ← | lactose permease |
| RA | 366,254 | C→A | E18* (GAA→TAA) | lacZ ← | beta‑galactosidase |
| RA | 400,527 | G→A | L133L (CTG→TTG) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 854,905 | C→T | V280V (GTG→GTA) | ldtB ← | L,D‑transpeptidase LdtB |
| RA | 934,781 | C→A | P520T (CCG→ACG) | ftsK → | cell division DNA translocase FtsK |
| RA | 935,346 | C→T | P708L (CCG→CTG) | ftsK → | cell division DNA translocase FtsK |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,049,827 | T→G | intergenic (‑83/‑6) | gfcA ← / → insA4 | threonine‑rich inner membrane protein GfcA/IS1 family protein InsA |
| RA | 1,098,620 | T→A | V245V (GTT→GTA) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,259,717 | C→T | A363T (GCC→ACC) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | 1,291,226 | C→T | R329* (CGA→TGA) | rssB → | regulator of RpoS |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,414,813 | G→A | R858R (CGC→CGT) | recE ← | exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific |
| RA | 1,462,306 | G→A | R61H (CGT→CAT) | paaK → | phenylacetate‑CoA ligase |
| RA | 1,532,490 | G→A | M225I (ATG→ATA) | ydcC → | H repeat‑associated putative transposase YdcC |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,885 | G→A | G40D (GGC→GAC) | rsxA → | SoxR [2Fe‑2S] reducing system protein RsxA |
| RA | 1,713,374 | C→T | R202R (CGC→CGT) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,791,414 | T→A | T203S (ACG→TCG) | rflP ← | anti‑FlhDC factor RflP |
| RA | 1,839,073 | C→T | A109A (GCC→GCT) | ynjD → | putative ABC transporter ATP‑binding protein YnjD |
| RA | 1,966,684 | C→T | L118L (CTG→CTA) | cheZ ← | chemotaxis protein CheZ |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,114,750 | G→A | Q383* (CAA→TAA) | wcaM ← | putative colanic acid biosynthesis protein WcaM |
| RA | 2,270,736 | G→A | R4H (CGC→CAC) | pdeN → | putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,324,857 | C→T | I34I (ATC→ATT) | atoE → | short chain fatty acid transporter |
| RA | 2,355,848 | C→T | P110S (CCA→TCA) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,426,454 | G→A | A112V (GCC→GTC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,464,151 | 2 bp→AA | intergenic (+81/+100) | yfdF → / ← mlaA | protein YfdF/intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA |
| RA | 2,495,182 | G→A | I37I (ATC→ATT) | yfdY ← | DUF2545 domain‑containing protein YfdY |
| RA | 2,518,034 | G→A | intergenic (‑202/+7) | pdeA ← / ← alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala |
| RA | 2,591,647 | G→A | R14H (CGC→CAC) | dapE → | succinyl‑diaminopimelate desuccinylase |
| RA | 2,638,365 | G→A | S96S (AGC→AGT) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,643,926 | A→G | S120P (TCT→CCT) | rlmN ← | 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase |
| RA | 2,661,885 | C→G | V83L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,665,920 | G→A | Q162Q (CAG→CAA) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 2,703,341 | G→A | R16C (CGT→TGT) | era ← | 30S ribosomal subunit maturation GTPase Era |
| RA | 2,710,158 | G→A | R3C (CGT→TGT) | rseD ← | rpoE leader peptide |
| RA | 2,715,294 | A→G | L9L (CTT→CTC) | yfiE ← | putative LysR‑type DNA‑binding transcriptional regulator YfiE |
| RA | 2,749,965 | G→A | E398K (GAG→AAG) | yfjD → | UPF0053 family inner membrane protein YfjD |
| RA | 2,814,688 | C→T | A16T (GCG→ACG) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,815,493 | G→A | S316F (TCT→TTT) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,838,265 | G→A | P334S (CCT→TCT) | ascG ← | DNA‑binding transcriptional repressor AscG |
| RA | 2,867,454 | 2 bp→CA | coding (97‑98/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,868,970 | G→A | R184C (CGT→TGT) | pcm ← | protein‑L‑isoaspartate O‑methyltransferase |
| RA | 2,896,144 | G→A | L138L (CTG→TTG) | ygcR ← | putative flavoprotein |
| RA | 2,935,489 | G→A | A419T (GCA→ACA) | fucP → | L‑fucose:H(+) symporter |
| RA | 2,960,700 | C→T | G577R (GGG→AGG) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,967,217 | C→T | Q406Q (CAG→CAA) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,974,399 | C→T | G539E (GGA→GAA) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyltransferase/acyl‑acyl carrier protein synthetase |
| RA | 2,999,120 | G→A | intergenic (‑63/+16) | glyU ← / ← actS | tRNA‑Gly/amidase activator |
| RA | 3,067,220 | T→A | intergenic (‑47/+120) | ygfI ← / ← yggE | putative DNA‑binding transcriptional regulator YgfI/DUF541 domain‑containing protein YggE |
| RA | 3,077,190 | C→T | Q89Q (CAG→CAA) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,111,571 | G→A | P140S (CCG→TCG) | yghE ← | putative type II secretion system L‑type protein YghE |
| RA | 3,112,119 | G→A | R311C (CGC→TGC) | yghF ← | putative type II secretion system C‑type protein YghF |
| RA | 3,127,343 | G→A | L227L (CTG→TTG) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,127,579 | G→A | P148L (CCT→CTT) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,178,904 | G→A | D264N (GAT→AAT) | tolC → | outer membrane channel TolC |
| RA | 3,220,841 | G→A | A450T (GCG→ACG) | patA → | putrescine aminotransferase |
| RA | 3,249,916 | G→A | P78P (CCG→CCA) | yqjE → | inner membrane protein YqjE |
| RA | 3,321,703 | G→A | intergenic (‑90/+369) | yhbX ← / ← leuU | putative hydrolase YhbX/tRNA‑Leu |
| RA | 3,322,707 | G→A | intergenic (‑202/+26) | secG ← / ← glmM | Sec translocon subunit SecG/phosphoglucosamine mutase |
| RA | 3,326,161 | G→T | Q259K (CAG→AAG) | ftsH ← | ATP‑dependent zinc metalloprotease FtsH |
| RA | 3,349,512 | C→T | E100K (GAG→AAG) | mtgA ← | peptidoglycan glycosyltransferase MtgA |
| RA | 3,349,949 | C→T | V171M (GTG→ATG) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,377,150 | C→A | V91F (GTT→TTT) | sspA ← | stringent starvation protein A |
| RA | 3,405,174 | C→T | intergenic (+716/‑262) | yhdH → / → accB | acrylyl‑CoA reductase/biotin carboxyl carrier protein |
| RA | 3,474,290 | T→C | K88R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,474,846 | A→G | G40G (GGT→GGC) | tusB ← | sulfurtransferase complex subunit TusB |
| RA | 3,490,113 | G→A | P23L (CCG→CTG) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,494,720 | T→G | I237S (ATC→AGC) | nirB → | nitrite reductase (NADH) large subunit |
| RA | 3,515,879 | C→T | G12E (GGG→GAG) | dam ← | DNA adenine methyltransferase |
| RA | 3,519,818 | C→T | E296K (GAA→AAA) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,520,507 | G→A | P66L (CCC→CTC) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,522,187 | C→T | A189T (GCG→ACG) | hofM ← | DNA utilization protein HofM |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,591,960 | C→T | P122P (CCG→CCA) | ugpB ← | sn‑glycerol 3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,642,761 | C→T | A124A (GCG→GCA) | rsmJ ← | 16S rRNA m(2)G1516 methyltransferase |
| RA | 3,707,096 | C→T | D204N (GAC→AAC) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| RA | 3,720,634 | G→A | intergenic (‑34/‑46) | hokA ← / → insJ | small toxic polypeptide/insertion element IS150 protein InsA |
| RA | 3,741,228 | C→T | D119N (GAT→AAT) | ysaA ← | putative electron transport protein YsaA |
| RA | 3,821,992 | C→T | R189C (CGC→TGC) | gmk → | guanylate kinase |
| RA | 3,830,800 | C→T | A115V (GCG→GTG) | yicH → | AsmA family protein YicH |
| RA | 3,844,914 | C→T | R317R (CGC→CGT) | adeD → | adenine deaminase |
| RA | 3,850,542 | C→T | G62D (GGT→GAT) | uhpA ← | DNA‑binding transcriptional activator UhpA |
| RA | 3,856,975 | C→T | R477H (CGC→CAC) | yidJ ← | putative sulfatase/phosphatase YidJ |
| RA | 3,931,995 | G→A | G227E (GGG→GAG) | kup → | K(+):H(+) symporter Kup |
| RA | 3,943,889 | G→A | noncoding (186/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,951,454 | G→T | intergenic (+897/‑747) | ilvX → / → ilvM | uncharacterized protein IlvX/acetolactate synthase II subunit IlvM |
| RA | 4,002,928 | G→A | T89I (ACA→ATA) | yigG ← | inner membrane protein |
| RA | 4,006,136 | G→A | A91A (GCG→GCA) | recQ → | ATP‑dependent DNA helicase RecQ |
| RA | 4,010,883 | C→T | G228G (GGC→GGT) | yigL → | phosphosugar phosphatase YigL |
| RA | 4,046,297 | G→A | N102N (AAC→AAT) | yihG ← | 1‑acylglycerol‑3‑phosphate O‑acyltransferase YihG |
| RA | 4,060,839 | G→A | W131* (TGG→TGA) | yihL → | putative DNA‑binding transcriptional regulator YihL |
| RA | 4,095,919 | C→T | D22N (GAT→AAT) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,109,941 | G→A | A4A (GCG→GCA) | cdh → | CDP‑diacylglycerol diphosphatase |
| RA | 4,135,006 | G→A | R391H (CGT→CAT) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,143,280 | G→A | A251T (GCG→ACG) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,240,295 | G→A | intergenic (‑240/‑30) | yjbT ← / → psiE | PF17089 family protein YjbT/putative phosphate starvation‑inducible protein PsiE |
| RA | 4,259,258 | G→A | G8S (GGT→AGT) | yjbJ → | putative stress response protein YjbJ |
| RA | 4,266,974 | G→A | intergenic (+113/‑140) | alr → / → tyrB | alanine racemase 1/tyrosine aminotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,321,884 | C→T | R180H (CGC→CAC) | phnF ← | putative transcriptional regulator PhnF |
| RA | 4,341,582 | C→T | R16H (CGC→CAC) | melR ← | DNA‑binding transcriptional dual regulator MelR |
| RA | 4,346,114 | C→T | D405N (GAC→AAC) | fumB ← | fumarase B |
| RA | 4,374,499 | C→T | intergenic (‑265/+130) | yjeJ ← / ← epmB | protein YjeJ/lysine 2,3‑aminomutase |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196359 | 1201650 | 5292 | 2 [1] | [1] 2 | [icd]–[ymfI] | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,[ymfI] |
| * | * | ÷ | NC_000913 | 1201758 | 1211413 | 9656 | 2 [1] | [1] 2 | [ymfI]–mcrA | [ymfI],ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 3423889–3424232 | 3424409–3424238 | 7–521 | 2 [1] | [1] 2 | rrlD | 23S ribosomal RNA |