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 | 42,108 | G→A | intergenic (‑177/‑295) | caiT ← / → fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| RA | 109,960 | G→A | R561H (CGT→CAT) | secA → | protein translocation ATPase |
| JC JC | 177,251 | IS2 (–) +5 bp | coding (370‑374/624 nt) | yadS ← | PF03458 family protein YadS |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| 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 | 363,292 | G→T | S1005* (TCG→TAG) | lacZ ← | beta‑galactosidase |
| RA | 399,639 | +A | coding (47/213 nt) | yaiZ → | DUF2754 domain‑containing protein YaiZ |
| JC JC | 458,790 | IS186 (+) +6 bp :: Δ1 bp | intergenic (+90/‑93) | clpX → / → lon | ATP‑dependent Clp protease ATP‑binding subunit ClpX/Lon protease |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 657,282 | G→A | intergenic (+165/‑10) | pagP → / → cspE | Lipid A palmitoyltransferase/transcription antiterminator and regulator of RNA stability CspE |
| JC JC | 663,262 | IS2 (–) +5 bp | coding (698‑702/1212 nt) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase DacA |
| 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 | 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 | 1,069,743 | C→T | A33T (GCA→ACA) | rutG ← | pyrimidine:H(+) symporter |
| 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 |
| JC JC | 1,190,264 | IS2 (+) +5 bp | coding (180‑184/672 nt) | 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 |
| RA | 1,265,018 | C→T | P3S (CCT→TCT) | prfA → | peptide chain release factor RF1 |
| RA | 1,272,743 | C→T | C79C (TGC→TGT) | chaC → | glutathione‑specific gamma‑glutamylcyclotransferase |
| RA | 1,278,959 | C→T | L335L (CTG→TTG) | narK → | nitrate:nitrite antiporter NarK |
| RA | 1,287,294 | C→A | noncoding (35/85 nt) | tyrV ← | tRNA‑Tyr |
| RA | 1,287,323 | C→T | noncoding (6/85 nt) | tyrV ← | tRNA‑Tyr |
| RA | 1,287,779 | C→T | intergenic (‑157/+3) | tyrT ← / ← purU | tRNA‑Tyr/formyltetrahydrofolate deformylase |
| RA | 1,295,985 | C→T | A713T (GCG→ACG) | adhE ← | fused acetaldehyde‑CoA dehydrogenase and iron‑dependent alcohol dehydrogenasealdehyde/alcohol dehydrogenase AdhE |
| RA | 1,298,624 | C→T | P9P (CCC→CCT) | ychE → | MarC family putative inner membrane protein YchE |
| 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 | 1,315,384 | G→A | Y129Y (TAC→TAT) | yciF ← | DUF892 domain‑containing protein YciF |
| RA | 1,317,129 | G→A | Q32* (CAG→TAG) | trpA ← | tryptophan synthase subunit alpha |
| RA | 1,322,325 | G→A | L208F (CTC→TTC) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,356,932 | G→A | T60I (ACC→ATC) | sapA ← | putative periplasmic binding protein SapA |
| 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 | 1,366,433 | G→A | G295D (GGC→GAC) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| RA | 1,400,978 | C→T | G266S (GGT→AGT) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| RA | 1,501,192 | C→T | P207L (CCT→CTT) | tehA → | tellurite resistance protein |
| RA | 1,610,076 | T→G | D202A (GAT→GCT) | uxaB ← | tagaturonate reductase |
| 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 | 1,655,795 | IS2 (–) +5 bp | intergenic (‑122/‑9) | ynfA ← / → ynfB | putative transporter YnfA/DUF1283 domain‑containing protein YnfB |
| RA | 1,711,338 | G→A | V171I (GTA→ATA) | rsxE → | SoxR [2Fe‑2S] reducing system protein RsxE |
| 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 | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,907,165 | IS150 (–) +4 bp :: +CA | intergenic (‑105/+58) | rlmA ← / ← cspC | 23S rRNA m(1)G745 methyltransferase/transcription antiterminator and regulator of mRNA stability CspC |
| 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 | 2,173,364 | Δ1 bp | intergenic (‑491/+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 | 2,405,969 | C→T | V225I (GTT→ATT) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| RA | 2,580,388 | G→A | P251P (CCG→CCA) | tktB → | transketolase 2 |
| JC JC | 2,737,689 | IS150 (+) +3 bp | intergenic (+43/‑54) | pheL → / → pheA | phe operon leader peptide/fused chorismate mutase/prephenate dehydratase |
| JC JC | 2,906,143 | IS5 (+) +4 bp | coding (433‑436/873 nt) | ygcG → | TPM domain‑containing protein YgcG |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,926,292 | C→T | intergenic (+96/‑16) | queF → / → ppnN | 7‑cyano‑7‑deazaguanine reductase/nucleotide 5'‑monophosphate nucleosidase |
| MC JC | 2,942,765 | Δ8 bp | noncoding (70‑77/206 nt) | gcvB → | small regulatory RNA GcvB |
| 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 |
| JC JC | 3,434,139 | IS2 (+) +5 bp | coding (450‑454/510 nt) | def → | peptide deformylase |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,554,539 | T→G | Y485* (TAT→TAG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,600,390 | G→A | Q132* (CAG→TAG) | rpoH ← | RNA polymerase sigma factor RpoH |
| RA | 3,608,416 | G→A | A656T (GCC→ACC) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,612,194 | G→A | E110E (GAG→GAA) | yhhT → | putative transporter YhhT |
| RA | 3,614,717 | G→A | G351S (GGC→AGC) | nikA → | Ni(2(+)) ABC transporter periplasmic binding protein |
| RA | 3,638,300 | G→A | G220D (GGC→GAC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,692,114 | C→T | S165N (AGC→AAC) | bcsB ← | cellulose synthase periplasmic subunit |
| 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 | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,808,243 | C→T | intergenic (‑5/‑297) | rirA ← / → waaA | small regulatory RNA RirA/KDO transferase |
| 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 | 3,907,139 | G→T | A147E (GCG→GAG) | phoU ← | negative regulator of the pho regulon |
| JC JC | 3,931,171 | IS4 (–) +12 bp | intergenic (‑78/‑134) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| JC JC | 3,938,725 | IS5 (–) +4 bp | coding (499‑502/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| JC JC | 3,960,601 | IS2 (+) +5 bp | intergenic (‑788/‑72) | ppiC ← / → rep | peptidyl‑prolyl cis‑trans isomerase C/ATP‑dependent DNA helicase Rep |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| 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 | 4,215,347 | 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 | 4,285,976 | IS150 (+) +3 bp | coding (1394‑1396/1959 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 |
| JC JC | 4,354,764 | IS2 (–) +5 bp | intergenic (‑47/+186) | lysU ← / ← dtpC | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase/dipeptide/tripeptide:H(+) symporter DtpC |
| 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 | 4,504,498 | T→C | G147G (GGT→GGC) | nanX → | sialic acid transporter NanX |
| 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 | 4,615,345 | C→T | G67S (GGC→AGC) | yjjW ← | putative glycyl‑radical enzyme activating enzyme YjjW |
| 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 | 257908 | 258682 | 775 | 26 [0] | [1] 2 | insB9–[crl] | insB9,insA9,[crl] |
| * | * | ÷ | NC_000913 | 390613 | 390662 | 50 | 2 [1] | [1] 2 | yaiT | putative autotransporter YaiT |
| * | * | ÷ | NC_000913 | 394418 | 394451 | 34 | 3 [0] | [1] 2 | [yaiT] | [yaiT] |
| * | * | ÷ | NC_000913 | 603800 | 606673 | 2874 | 16 [0] | [0] 2 | [ybdG]–[ybdK] | [ybdG],nfsB,ybdF,ybdJ,[ybdK] |
| * | * | ÷ | NC_000913 | 606805 | 607156 | 352 | 2 [1] | [0] 2 | ybdK | putative glutamate‑‑cysteine ligase 2 |
| * | * | ÷ | NC_000913 | 607316 | 607764 | 449 | 2 [0] | [0] 11 | [ybdK]–[sokE] | [ybdK],[sokE] |
| * | * | ÷ | NC_000913 | 686008 | 686083 | 76 | 2 [1] | [1] 3 | gltJ | glutamate/aspartate ABC transporter membrane subunit GltJ |
| * | * | ÷ | NC_000913 | 1196347 | 1200407 | 4061 | 2 [1] | [1] 2 | [icd]–[intE] | [icd],C0293,ymfD,ymfE,lit,[intE] |
| * | * | ÷ | NC_000913 | 1200471 | 1211428 | 10958 | 2 [1] | [1] 2 | [intE]–mcrA | [intE],xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1219479 | 1219517 | 39 | 2 [1] | [1] 2 | ymgF/ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| * | * | ÷ | NC_000913 | 1292950 | 1293008 | 59 | 2 [1] | [1] 2 | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| * | * | ÷ | NC_000913 | 1530415 | 1530545 | 131 | 2 [1] | [1] 2 | [yncO] | [yncO] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 21 [0] | [0] 9 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2903685 | 2903832 | 148 | 2 [1] | [0] 2 | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| * | * | ÷ | NC_000913 | 3423880–3424422 | 3424422 | 1–543 | 2 [1] | [1] 2 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035403–4035731 | 4036863–4035735 | 5–1461 | 2 [1] | [1] 2 | [rrsA] | [rrsA] |
| * | * | ÷ | NC_000913 | 4166876–4168219 | 4168497 | 279–1622 | 2 [1] | [1] 2 | [rrsB]–gltT | [rrsB],gltT |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 26 (1.010) | 25/474 | 0.2 | 100% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 603799 | 0 (0.000) | 16 (0.600) | 15/490 | 0.6 | 100% | coding (865/1248 nt) | ybdG | miniconductance mechanosensitive channel YbdG |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 607765 = | 0 (0.000) | 11 (0.420) | 10/488 | 1.0 | 100% | noncoding (28/60 nt) | sokE | small RNA SokE |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 21 (0.790) | 18/490 | 0.4 | 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 | 1979271 = | 0 (0.000) | 8 (0.300) | 8/490 | 1.3 | 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 | |||||