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 | 90,999 | T→C | S302S (AGT→AGC) | rsmH → | 16S rRNA m(4)C1402 methyltransferase |
| RA | 92,439 | G→A | D343N (GAC→AAC) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 96,855 | G→A | R285H (CGT→CAT) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| RA | 97,933 | G→A | A283T (GCA→ACA) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase |
| RA | 109,960 | G→A | R561H (CGT→CAT) | secA → | protein translocation ATPase |
| RA | 122,183 | G→A | G31D (GGC→GAC) | pdhR → | DNA‑binding transcriptional dual regulator PdhR |
| 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 | 363,292 | G→T | S1005* (TCG→TAG) | lacZ ← | beta‑galactosidase |
| RA | 402,615 | G→A | W290* (TGG→TAG) | phoA → | alkaline phosphatase |
| RA | 418,124 | T→C | L79S (TTA→TCA) | phoR → | sensor histidine kinase PhoR |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| RA | 657,282 | G→A | intergenic (+165/‑10) | pagP → / → cspE | Lipid A palmitoyltransferase/transcription antiterminator and regulator of RNA stability CspE |
| 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 | 793,050 | C→T | E247K (GAA→AAA) | modF ← | ABC family protein ModF |
| RA | 797,412 | C→T | P287S (CCG→TCG) | modC → | molybdate ABC transporter ATP binding subunit |
| RA | 802,225 | C→T | A113A (GCC→GCT) | ybhI → | putative tricarboxylate transporter |
| 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 | 1,112,187 | C→T | A442V (GCC→GTC) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,113,668 | C→T | G30G (GGC→GGT) | yceK → | DUF1375 domain‑containing lipoprotein YceK |
| RA | 1,121,088 | C→T | intergenic (‑133/+154) | bssS ← / ← dinI | regulator of biofilm formation/DNA damage‑inducible protein I |
| RA | 1,121,702 | C→T | Q302Q (CAG→CAA) | pyrC ← | dihydroorotase |
| RA | 1,125,988 | G→A | A143T (GCT→ACT) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,126,625 | G→A | G157S (GGT→AGT) | yceH → | DUF480 domain‑containing protein YceH |
| RA | 1,159,343 | C→T | intergenic (+41/+19) | ptsG → / ← fhuE | glucose‑specific PTS enzyme IIBC component/ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,169,410 | C→T | intergenic (+8/+2) | bhsB → / ← ldtC | small RNA BhsB/L,D‑transpeptidase LdtC |
| 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 |
| 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 |
| MC JC | 1,287,294 | 295 bp→A | [tyrV]–[tyrT] | [tyrV], [tyrT] | |
| 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 | 1,501,192 | 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 | 1,746,495 | +T | noncoding (61/77 nt) | valV → | tRNA‑Val |
| 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 |
| RA | 1,976,539 | G→A | L201F (CTT→TTT) | motA ← | motility protein A |
| 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 | 2,241,519 | A→T | N50K (AAT→AAA) | galS ← | DNA‑binding transcriptional dual regulator GalS |
| RA | 2,395,372 | G→A | S175S (AGC→AGT) | nuoJ ← | NADH:quinone oxidoreductase subunit J |
| 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 |
| RA | 2,614,394 | G→A | G154D (GGC→GAC) | focB → | formate channel FocB |
| 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 |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,270,356 | G→A | noncoding (237/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,277,998 | G→A | S223F (TCC→TTC) | agaR ← | DNA‑binding transcriptional repressor AgaR |
| 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 | 3,474,425 | 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 | 3,638,268 | G→A | W209* (TGG→TGA) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,638,300 | G→A | G220D (GGC→GAC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,651,284 | G→A | intergenic (+622/‑7) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| 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 | 3,728,611 | C→T | G254E (GGG→GAG) | xylB ← | xylulokinase |
| RA | 3,752,764 | G→A | S258N (AGC→AAC) | yiaU → | putative DNA‑binding transcriptional regulator YiaU |
| RA | 3,756,810 | G→A | L340L (CTA→TTA) | yiaY ← | L‑threonine dehydrogenase |
| 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 | 3,848,618 | G→A | P3S (CCG→TCG) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| 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 |
| RA | 3,937,525 | G→A | A78T (GCC→ACC) | rbsK → | ribokinase |
| 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 | 4,171,438 | Δ2 bp | noncoding (2798‑2799/2904 nt) | rrlB → | 23S ribosomal RNA |
| 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 |
| 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 | 1196314 | 1211521 | 15208 | 3 [2] | [0] 3 | [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 | 1397311 | 1427512 | 30202 | 4 [2] | [0] 35 | ynaJ–[lomR] | ynaJ,uspE,fnr,ogt,abgT,abgB,abgA,abgR,mcaS,smrA,dgcM,ynaN,zntB,fnrS,ynaL,dbpA,ttcA,intR,xisR,rcbA,ralA,ralR,recT,recE,racC,ydaE,kilR,kilS,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzoR,trkG,ynaK,ydaY,ynaA,[lomR] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 28 [0] | [0] 25 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423906–3424233 | 3424415–3424238 | 6–510 | 3 [1] | [2] 3 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4166882–4168251 | 4168479–4168465 | 215–1598 | 3 [2] | [2] 3 | [rrsB]–gltT | [rrsB],gltT |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 28 (0.550) | 28/482 | 0.6 | 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 | = 1397325 | NA (NA) | 34 (0.670) | 32/482 | 0.5 | 100% | intergenic (+233/‑40) | insH4/ynaJ | IS5 family transposase and trans‑activator/DUF2534 domain‑containing protein YnaJ |
| ? | NC_000913 | 1427513 = | 0 (0.000) | pseudogene (125/210 nt) | lomR | Rac prophage; protein LomR_1 | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 25 (0.490) | 25/482 | 0.7 | 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 | |||||