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 | 109,960 | G→A | R561H (CGT→CAT) | secA → | protein translocation ATPase |
| 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 | 455,661 | T→C | F177L (TTC→CTC) | tig → | trigger factor |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| MC JC | 674,957 | Δ12,894 bp | IS5‑mediated | ybeL–gltI | ybeL, ybeQ, ybeR, djlB, ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| 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 | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 987,174 | (A)6→5 | intergenic (‑192/+411) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| JC JC | 1,034,134 | IS30 (–) +2 bp | coding (881‑882/1794 nt) | hyaB → | hydrogenase 1 large subunit |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| 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 | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,666,974 | IS30 (+) +2 bp | coding (245‑246/696 nt) | bidA ← | dethiobiotin synthetase BidA |
| JC JC | 1,666,983 | IS30 (+) +2 bp | coding (236‑237/696 nt) | bidA ← | dethiobiotin synthetase BidA |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,765,675 | G→A | T1004M (ACG→ATG) | ydiJ ← | putative FAD‑linked oxidoreductase YdiJ |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,910,136 | IS30 (+) +2 bp | intergenic (‑37/‑139) | kdgR ← / → yebQ | DNA‑binding transcriptional repressor KdgR/putative transporter YebQ |
| RA | 1,987,499 | C→A | intergenic (+71/+8) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,188,087 | T→C | T110A (ACG→GCG) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,384,808 | C→T | K305K (AAG→AAA) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,410,419 | G→A | L312L (CTG→TTG) | yfbS ← | putative transporter YfbS |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| JC JC | 2,490,650 | IS5 (–) +4 bp | coding (1298‑1301/1695 nt) | oxc ← | oxalyl‑CoA decarboxylase |
| JC JC | 2,570,713 | IS30 (+) +2 bp | coding (1038‑1039/1404 nt) | eutE ← | acetaldehyde dehydrogenase (acetylating) EutE |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,934,134 | A→C | intergenic (‑446/‑101) | fucA ← / → fucP | L‑fuculose‑phosphate aldolase/L‑fucose:H(+) symporter |
| JC JC | 3,063,112 | IS30 (+) +2 bp | coding (126‑127/996 nt) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,336,411 | 2 bp→AT | coding (83‑84/1260 nt) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,444,905 | C→T | G109S (GGT→AGT) | rpsE ← | 30S ribosomal subunit protein S5 |
| RA | 3,465,502 | G→A | E141K (GAG→AAG) | gspM → | Type II secretion system protein GspM |
| RA | 3,474,424 | T→G | K43N (AAA→AAC) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,486,456 | A→C | I113L (ATT→CTT) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,502 | C→T | T128I (ACT→ATT) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,552 | G→A | A145T (GCA→ACA) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,553,107 | G→T | S8I (AGT→ATT) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,610,880 | IS30 (+) +2 bp | coding (853‑854/1218 nt) | yhhS ← | putative transporter YhhS |
| JC JC | 3,639,755 | IS150 (+) +3 bp | intergenic (‑35/‑354) | uspB ← / → uspA | universal stress protein B/universal stress protein A |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,707,883 | G→A | intergenic (‑178/+733) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,708,467 | Δ168 bp | [proK] | [proK] | |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC | 3,822,651 | (CAGGAT)1→2 | coding (252/2109 nt) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,162 | C→T | H255Y (CAC→TAC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| RA | 3,878,536 | G→A | Y528Y (TAC→TAT) | gyrB ← | DNA gyrase subunit B |
| MC JC | 3,991,548 | Δ200 bp | coding (396‑595/2547 nt) | cyaA → | adenylate cyclase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 3,996,049 | T→A | L156* (TTG→TAG) | yigA → | DUF484 domain‑containing protein YigA |
| RA | 4,011,802 | C→T | P243S (CCG→TCG) | bioP → | biotin transporter |
| RA | 4,084,903 | T→G | N307T (AAC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,092,703 | A→G | F41L (TTC→CTC) | frvA ← | putative PTS enzyme IIA component FrvA |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,161,248 | G→T | G61V (GGC→GTC) | fabR → | DNA‑binding transcriptional repressor FabR |
| RA | 4,164,123 | C→G | A162G (GCA→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,189,451 | Δ1 bp | coding (4102/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,282,332 | (A)5→6 | coding (744/1293 nt) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| 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 |
| JC JC | 4,640,418 | IS30 (–) +2 bp | coding (17‑18/141 nt) | yjjY → | uncharacterized protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211475 | 15199 | 46 [44] | [44] 46 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978504 | 10–776 | 130 [0] | [0] 168 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423762–3424232 | 3424512–3424238 | 7–751 | 45 [44] | [44] 45 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3930995 | 3938724 | 7730 | 111 [0] | [0] 104 | [ravA]–[rbsR] | [ravA],kup,rbsD,rbsA,rbsC,rbsB,rbsZ,rbsK,[rbsR] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1095166 = | NA (NA) | 135 (1.200) | 95/598 | 0.0 | NA | noncoding (337/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1095167 | NA (NA) | 82 (0.730) | 59/598 | 0.7 | NA | noncoding (336/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 130 (1.160) | 79/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 68 (0.610) | 43/598 | 1.7 | 58.6% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 3265225 = | 48 (0.430) | coding (804/990 nt) | tdcB | catabolic threonine dehydratase | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 68 (0.610) | 55/598 | 0.9 | 73.9% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 3560169 = | 24 (0.210) | intergenic (+303/+453) | rtcR/glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 95 (0.850) | 63/598 | 0.5 | 73.1% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4117985 | 35 (0.310) | coding (106/846 nt) | glpF | glycerol facilitator | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 35 (0.310) | 32/598 | 2.9 | 21.3% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1555644 | 129 (1.150) | coding (26/1698 nt) | maeA | malate dehydrogenase (oxaloacetate‑decarboxylating) | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 48 (0.430) | 36/598 | 2.4 | 48.5% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2945061 = | 51 (0.450) | coding (782/807 nt) | tcdA | tRNA threonylcarbamoyladenosine dehydratase | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 101 (0.910) | 74/594 | 0.2 | 80.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 3560170 | 25 (0.220) | intergenic (+304/+452) | rtcR/glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 168 (1.500) | 97/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 111 (0.990) | 67/598 | 0.4 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3930994 | 0 (0.000) | coding (100/1497 nt) | ravA | regulatory ATPase RavA | |||||
| * | ? | NC_000913 | = 3265226 | 47 (0.420) | 121 (1.080) | 81/596 | 0.1 | 72.0% | coding (803/990 nt) | tdcB | catabolic threonine dehydratase |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 103 (0.920) | 72/596 | 0.3 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3938725 = | 0 (0.000) | coding (499/993 nt) | rbsR | DNA‑binding transcriptional dual regulator RbsR | |||||
| * | ? | NC_000913 | 4117984 = | 34 (0.300) | 95 (0.850) | 69/594 | 0.3 | 73.6% | coding (107/846 nt) | glpF | glycerol facilitator |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 96 (0.850) | 60 (0.550) | 45/580 | 1.4 | 39.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 93 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 111 (0.990) | 54 (0.500) | 37/580 | 2.1 | 35.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 93 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||