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 |
| JC | 14,775 | (ATGGTC)2→1 | coding (608‑613/1131 nt) | dnaJ → | chaperone protein DnaJ |
| 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 | 466,169 | T→A | T382S (ACC→TCC) | ybaE ← | uncharacterized protein YbaE |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 634,096 | A→G | T171A (ACT→GCT) | ybdL → | methionine transaminase |
| MC JC | 676,617 | Δ11,234 bp | IS5‑mediated | ybeR–gltI | 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 |
| JC JC | 880,332 | IS5 (–) +4 bp | coding (146‑149/627 nt) | gstB ← | glutathione S‑transferase GstB |
| 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 | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| 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 | 1,196,220 | 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 |
| JC | 1,333,261 | Δ8 bp | coding (2214‑2221/2598 nt) | topA → | DNA topoisomerase 1 |
| 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 |
| MC JC | 1,651,549 | Δ20,154 bp | IS2‑mediated | ynfP–asr | 19 genes ynfP, rspB, rspA, ynfA, ynfB, speG, ynfC, ynfD, ynfE, ynfF, ynfG, ynfH, dmsD, clcB, bidA, mlc, ynfL, ynfM, asr |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,856,968 | T→A | I268F (ATT→TTT) | ydjI ← | L‑glycero‑L‑galacto‑octuluronate‑1‑phosphate aldolase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 2,003,242 | T→G | E122A (GAA→GCA) | fliC ← | flagellar filament structural protein |
| 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 | 2,201,392 | G→C | D372H (GAT→CAT) | yehI → | DUF4132 domain‑containing protein YehI |
| 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 |
| JC | 2,414,824 | (CTTGGCGTGATCCGTGCA)1→2 | coding (78/2145 nt) | pta → | phosphate acetyltransferase |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| 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 | 3,344,417 | T→G | F158L (TTT→TTG) | lptB → | lipopolysaccharide transport system ATP binding protein LptB |
| 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 |
| JC JC | 3,485,920 | IS2 (–) +5 bp | intergenic (‑102/‑196) | yhfA ← / → crp | OsmC family protein YhfA/DNA‑binding transcriptional dual regulator CRP |
| JC | 3,486,682 | +AAT | coding (563/633 nt) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,691 | T→A | L191Q (CTG→CAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,629,921 | C→T | E228K (GAG→AAG) | yhiI ← | putative membrane fusion protein YhiI |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,761,230 | G→A | S7F (TCC→TTC) | selA ← | selenocysteine synthase |
| 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 |
| RA | 3,912,074 | G→A | S532F (TCC→TTC) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| JC JC | 3,939,119 | IS2 (+) +5 bp | coding (893‑897/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,967,066 | C→T | T217I (ACC→ATC) | rho → | transcription termination factor Rho |
| 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 | 4,031,457 | C→T | F99F (TTC→TTT) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,031,511 | C→T | S117S (AGC→AGT) | pepQ → | Xaa‑Pro dipeptidase |
| 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 | 4,215,347 | 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 |
| JC JC | 4,287,188 | IS4 (–) +11 bp | coding (174‑184/1959 nt) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| 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 | 4,499,661 | T→C | intergenic (+161/‑1599) | insD6 → / → yjgZ | IS2 insertion element protein InsB/uncharacterized protein YjgZ |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 275509 | 363229 | 87721 | 94 [0] | [32] 37 | [mmuP]–lacY | [mmuP],mmuM,afuC,insB2,insA2,yagB,yagA,yagE,yagF,yagG,yagH,xynR,argF,argL,ykgS,insB3,insA3,yagJ,yagK,yagL,yagM,ykgV,yagN,intF,yagP,paoD,paoC,paoB,paoA,yagU,ykgJ,ecpE,ecpD,ecpC,ecpB,ecpA,matA,ykgL,ykgO,ykgM,ykgR,insE1,insF1,rclC,rclB,rclA,rclR,ykgE,ykgF,ykgG,ykgH,betA,betB,betI,betT,yahV,pdeL,yahB,yahC,yahD,yahE,yahF,yahG,yahH,yahI,yahJ,yahK,yahL,yahM,yahN,yahO,prpR,prpB,prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,cynX,lacA,lacY |
| * | * | ÷ | NC_000913 | 367084 | 372748 | 5665 | 35 [30] | [3] 98 | [lacI]–[mhpD] | [lacI],mhpR,mhpA,mhpB,mhpC,[mhpD] |
| * | * | ÷ | NC_000913 | 1196277 | 1211459 | 15183 | 38 [34] | [33] 36 | [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 | 776 | 112 [0] | [0] 120 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423806–3424233 | 3424482–3424238 | 6–677 | 36 [34] | [34] 37 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3708467 | 3708621 | 155 | 69 [0] | [31] 38 | [proK] | [proK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 275508 | 0 (0.000) | 94 (0.920) | 61/578 | 0.3 | 100% | coding (184/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter |
| ? | NC_000913 | 372749 = | 0 (0.000) | coding (635/810 nt) | mhpD | 2‑hydroxypentadienoate hydratase | |||||
| * | ? | NC_000913 | = 566774 | 107 (1.010) | 87 (0.830) | 41/594 | 1.3 | 43.7% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 118 (1.120) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 112 (1.060) | 73/598 | 0.2 | 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) | 63 (0.600) | 43/596 | 1.2 | 75.9% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1909271 = | 20 (0.190) | intergenic (+107/+37) | yobH/kdgR | uncharacterized protein YobH/DNA‑binding transcriptional repressor KdgR | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 108 (1.030) | 67/592 | 0.2 | 88.5% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1909272 | 14 (0.130) | intergenic (+108/+36) | yobH/kdgR | uncharacterized protein YobH/DNA‑binding transcriptional repressor KdgR | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 120 (1.130) | 82/598 | 0.1 | 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 | = 3708466 | 0 (0.000) | 68 (1.010) | 37/382 | 0.5 | 100% | intergenic (‑761/+150) | dppA/proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| ? | NC_000913 | 3708635 = | 0 (0.000) | noncoding (58/77 nt) | proK | tRNA‑Pro | |||||