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 |
| MC JC | 167,570 | Δ4 bp | coding (87‑90/2244 nt) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 192,437 | A→G | K195E (AAA→GAA) | pyrH → | UMP kinase |
| RA | 193,723 | T→A | M68K (ATG→AAG) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| RA | 224,625 | T→A | noncoding (855/1542 nt) | rrsH → | 16S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 262,854 | G→A | intergenic (+98/‑17) | proA → / → thrW | glutamate‑5‑semialdehyde dehydrogenase/tRNA‑Thr |
| 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 | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 553,161 | G→A | intergenic (‑61/+57) | purE ← / ← lpxH | N(5)‑carboxyaminoimidazole ribonucleotide mutase/UDP‑2,3‑diacylglucosamine diphosphatase |
| 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 |
| JC JC | 789,812 | IS2 (–) +5 bp | coding (164‑168/1149 nt) | galK ← | galactokinase |
| RA | 791,688 | G→A | S123F (TCC→TTC) | galE ← | UDP‑glucose 4‑epimerase |
| 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 |
| JC JC | 1,093,481 | IS2 (+) +5 bp | coding (606‑610/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,100,070 | G→A | C144Y (TGT→TAT) | ycdY → | chaperone protein YcdY |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,123,556 | C→T | E167K (GAA→AAA) | grxB ← | reduced glutaredoxin 2 |
| 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,316 | T→A | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,325 | A→G | K401K (AAA→AAG) | 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 | 1,331,947 | C→T | G300G (GGC→GGT) | 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 | 1,412,897 | G→A | L113L (CTC→CTT) | intR ← | putative integrase |
| RA | 1,428,087 | C→T | E214K (GAG→AAG) | insH5 ← | IS5 family transposase and trans‑activator |
| MC JC | 1,588,756 | Δ970 bp | [ydeS]–[ydeT] | [ydeS], [ydeT] | |
| RA | 1,610,076 | T→G | D202A (GAT→GCT) | uxaB ← | tagaturonate reductase |
| RA | 1,610,440 | C→T | E81K (GAA→AAA) | uxaB ← | tagaturonate reductase |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| JC JC | 1,651,851 | IS2 (–) +5 bp | intergenic (+1866/+873) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| MC JC | 1,704,350 | Δ390 bp | blr | blr | |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,738,377 | C→T | H178H (CAC→CAT) | purR → | DNA‑binding transcriptional repressor PurR |
| 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 | 1,975,224 | G→A | A34V (GCG→GTG) | cheA ← | chemotaxis protein CheA |
| RA | 1,987,499 | C→A | intergenic (+71/+8) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 2,003,276 | A→C | S111A (TCT→GCT) | fliC ← | flagellar filament structural protein |
| RA | 2,003,462 | C→A | A49S (GCG→TCG) | 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 | 2,175,991 | T→A | K111* (AAG→TAG) | gatZ ← | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone |
| RA | 2,188,087 | T→C | T110A (ACG→GCG) | yehA ← | putative fimbrial adhesin YehA |
| MC JC | 2,238,416 | Δ19 bp | coding (856‑874/1521 nt) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,263,441 | Δ1 bp | coding (55/1131 nt) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | 2,280,520 | T→G | intergenic (‑37/‑112) | rsuA ← / → radD | 16S rRNA pseudouridine(516) synthase/putative DNA repair helicase RadD |
| 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 |
| RA | 2,700,747 | G→A | L84L (CTC→CTT) | acpS ← | holo‑[acyl‑carrier‑protein] synthase |
| RA | 2,748,396 | G→A | A145A (GCG→GCA) | ypjD → | cytochrome c assembly family protein |
| RA | 2,756,976 | G→A | R273Q (CGA→CAA) | intA → | integrase IntA |
| RA | 2,780,060 | G→A | H889H (CAC→CAT) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,792,209 | G→A | V313M (GTG→ATG) | gabD → | succinate‑semialdehyde dehydrogenase (NADP(+)) GabD |
| RA | 2,800,435 | G→A | G97D (GGT→GAT) | ygaM → | DUF883 domain‑containing protein YgaM |
| RA | 2,810,925 | G→A | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator MprA |
| RA | 2,817,850 | G→A | noncoding (11/77 nt) | argQ ← | tRNA‑Arg |
| RA | 2,825,328 | G→A | S83S (TCC→TCT) | mltB ← | membrane‑bound lytic murein transglycosylase B |
| RA | 2,841,238 | G→A | M83I (ATG→ATA) | ascB → | 6‑phospho‑beta‑glucosidase AscB |
| RA | 2,863,773 | C→T | L61F (CTT→TTT) | ygbL → | putative 3‑oxo‑tetronate 4‑phosphate decarboxylase YgbL |
| RA | 2,878,077 | C→T | intergenic (+459/+492) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,889,365 | C→T | K245K (AAG→AAA) | cysI ← | sulfite reductase, hemoprotein subunit |
| RA | 2,905,825 | C→T | Q39* (CAA→TAA) | 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 |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,336,411 | 2 bp→AT | coding (83‑84/1260 nt) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,367,944 | G→A | A40T (GCG→ACG) | yhcG → | DUF1016 domain‑containing protein YhcG |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,399,929 | A→T | L17Q (CTG→CAG) | mreC ← | cell shape determining protein MreC |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,449,779 | G→A | S35S (AGC→AGT) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,468,768 | C→T | W362* (TGG→TGA) | chiA ← | endochitinase |
| RA | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,543,877 | G→A | P237P (CCG→CCA) | rpnA → | recombination‑promoting nuclease RpnA |
| 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 | 3,696,909 | G→A | G151E (GGA→GAA) | bcsE → | c‑di‑GMP‑binding protein BcsE |
| 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 | 3,761,230 | 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 | 3,883,678 | G→A | P18S (CCA→TCA) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | 3,912,074 | G→A | S532F (TCC→TTC) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,999,664 | C→T | S561L (TCG→TTG) | uvrD → | DNA helicase II |
| RA | 4,009,698 | G→A | A177T (GCA→ACA) | pldB → | lysophospholipase L2 |
| RA | 4,012,448 | T→C | K123K (AAA→AAG) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,012,454 | Δ1 bp | coding (363/954 nt) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,017,197 | C→T | intergenic (+5/‑136) | udp → / → rmuC | uridine phosphorylase/putative recombination limiting protein RmuC |
| 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 | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,156,839 | G→A | intergenic (+50/‑11) | argB → / → argH | acetylglutamate kinase/argininosuccinate lyase |
| RA | 4,157,116 | Δ1 bp | coding (267/1374 nt) | argH → | argininosuccinate lyase |
| RA | 4,208,132 | G→A | intergenic (‑600/‑15) | purH ← / → rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| 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 | 4,425,688 | 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 | 4,436,956 | 2 bp→TT | coding (202‑203/741 nt) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| 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 | 4,578,548 | G→A | Q264* (CAG→TAG) Q264* (CAG→TAG) |
mcrB ← mcrB ← |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
| RA | 4,585,230 | A→G | L511P (CTG→CCG) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| 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 | 1196344 | 1211431 | 15088 | 25 [24] | [24] 26 | [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 | 113 [0] | [0] 110 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423784–3424229 | 3424482–3424238 | 10–699 | 25 [24] | [23] 26 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762389–3764074 | 3765177–3764080 | 7–2789 | 26 [24] | [23] 25 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 113 (1.410) | 74/588 | 0.0 | 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) | 110 (1.380) | 69/588 | 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 | |||||