mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 26,293 | C→T | A6V (GCC→GTC) | ispH → | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate reductase |
| RA | 94,771 | T→C | V41A (GTT→GCT) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 127,249 | A→G | I519V (ATC→GTC) | aceF → | pyruvate dehydrogenase, E2 subunit |
| RA | 203,285 | A→G | T242T (ACA→ACG) | lpxA → | UDP‑N‑acetylglucosamine acyltransferase |
| RA | 220,720 | A→G | V70A (GTT→GCT) | metQ ← | L‑methionine/D‑methionine ABC transporter membrane anchored binding protein |
| RA | 276,826 | C→T | L38L (CTG→TTG) | mmuM → | homocysteine S‑methyltransferase |
| RA | 285,647 | (G)6→5 | coding (253/1383 nt) | yagG → | putative D‑xylonate transporter YagG |
| RA | 438,049 | A→G | G29G (GGT→GGC) | yajO ← | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
| RA | 554,040 | A→G | V133A (GTA→GCA) | ppiB ← | peptidyl‑prolyl cis‑trans isomerase B |
| RA | 570,683 | T→C | intergenic (+255/‑210) | ybcK → / → ybcL | DLP12 prophage; putative recombinase/DLP12 prophage; periplasmic protein YbcL |
| RA | 585,613 | T→C | G7G (GGA→GGG) | ompT ← | outer membrane protease VII (outer membrane protein 3b) |
| RA | 611,457 | A→G | G346G (GGT→GGC) | fepA ← | ferric enterobactin outer membrane transporter |
| RA | 647,184 | A→G | V109A (GTA→GCA) | citG ← | triphosphoribosyl‑dephospho‑CoA synthase |
| RA | 657,402 | G→A | Q37Q (CAG→CAA) | cspE → | transcription antiterminator and regulator of RNA stability |
| RA | 674,408 | C→T | A126T (GCA→ACA) | leuS ← | leucine‑‑tRNA ligase |
| RA | 828,399 | T→C | T195A (ACC→GCC) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 833,235 | A→G | T56A (ACC→GCC) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 840,914 | A→G | G206G (GGT→GGC) | fiu ← | putative iron siderophore outer membrane transporter |
| RA | 879,250 | G→A | R170H (CGC→CAC) | yliI → | aldose sugar dehydrogenase YliI |
| RA | 918,623 | A→G | G166G (GGT→GGC) | ybjX ← | DUF535 domain‑containing protein YbjX |
| RA | 1,125,608 | A→G | D16G (GAC→GGC) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,131,622 | T→C | V62A (GTA→GCA) | flgC → | flagellar basal‑body rod protein FlgC |
| RA | 1,163,202 | A→G | T189A (ACC→GCC) | lpoB → | outer membrane lipoprotein ‑ activator of MrcB activity |
| RA | 1,175,572 | A→G | N49S (AAC→AGC) | lolC → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,195,359 | T→C | G79G (GGT→GGC) | icd → | isocitrate dehydrogenase |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,225,965 | (G)5→6 | coding (116/696 nt) | minC ← | Z‑ring positioning protein MinC |
| RA | 1,276,275 | C→T | L448L (TTG→TTA) | narX ← | sensory histidine kinase NarX |
| RA | 1,349,544 | T→C | V188V (GTA→GTG) | yciW ← | putative oxidoreductase |
| RA | 1,351,196 | (G)7→6 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,355,008 | G→A | P155S (CCG→TCG) | sapB ← | putrescine ABC exporter membrane subunit SapB |
| RA | 1,358,224 | C→T | D322N (GAC→AAC) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,445,632 | A→G | N861S (AAC→AGC) | ydbH → | PF11739 family protein YdbH |
| RA | 1,456,973 | A→G | T182A (ACC→GCC) | paaE → | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| RA | 1,477,512 | T→C | intergenic (+62/‑109) | ydbD → / → ynbA | DUF2773 domain‑containing protein YdbD/putative inner membrane protein |
| RA | 1,483,429 | A→G | G123G (GGA→GGG) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,501,661 | A→G | T34A (ACG→GCG) | tehB → | tellurite methyltransferase |
| RA | 1,538,954 | T→C | T1213A (ACC→GCC) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,580,153 | A→G | V213A (GTG→GCG) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,589,600 | G→A | G134G (GGC→GGT) | ydeT ← | fimbrial usher domain‑containing protein YdeT |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,723,862 | T→C | V581A (GTT→GCT) | ydhK → | putative transporter YdhK |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,939,288 | C→T | L302L (TTG→TTA) | lpxM ← | myristoyl‑acyl carrier protein‑dependent acyltransferase |
| RA | 1,959,168 | (C)6→7 | coding (99/747 nt) | cutC ← | protein CutC |
| RA | 1,977,978 | T→C | T74A (ACG→GCG) | flhD ← | DNA‑binding transcriptional dual regulator FlhD |
| RA | 2,033,943 | T→C | intergenic (+204/‑108) | rseX → / → yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| RA | 2,087,186 | T→C | intergenic (‑72/+143) | yoeI ← / ← yeeY | uncharacterized protein YoeI/putative DNA‑binding transcriptional regulator YeeY |
| RA | 2,100,028 | T→C | N414S (AAC→AGC) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,154,657 | T→C | G214G (GGT→GGC) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,172,249 | T→C | T209A (ACA→GCA) | gatD ← | galactitol‑1‑phosphate 5‑dehydrogenase |
| RA | 2,177,086 | T→C | N40S (AAC→AGC) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY |
| RA | 2,198,933 | G→A | intergenic (+1635/‑1346) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,211,494 | T→C | G90G (GGT→GGC) | yehR → | DUF1307 domain‑containing lipoprotein YehR |
| RA | 2,247,916 | G→A | A206V (GCG→GTG) | lysP ← | lysine:H(+) symporter |
| RA | 2,285,709 | T→C | V445A (GTG→GCG) | yejM → | putative cardiolipin transport protein |
| RA | 2,316,298 | T→C | L41P (CTG→CCG) | rcsB → | DNA‑binding transcriptional activator RcsB |
| RA | 2,329,734 | T→C | T22A (ACG→GCG) | yfaQ ← | tandem DUF2300 domain‑containing protein YfaQ |
| RA | 2,387,912 | (T)6→7 | coding (515/717 nt) | yfbN ← | uncharacterized protein YfbN |
| RA | 2,397,384 | A→G | V20A (GTG→GCG) | nuoH ← | NADH:quinone oxidoreductase subunit H |
| RA | 2,432,464 | T→C | D160G (GAC→GGC) | folC ← | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase |
| RA | 2,447,463 | T→C | N4S (AAC→AGC) | aroC ← | chorismate synthase |
| RA | 2,590,698 | G→A | R1035H (CGC→CAC) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,685,824 | (A)7→8 | intergenic (‑317/‑11) | glyA ← / → hmp | serine hydroxymethyltransferase/nitric oxide dioxygenase |
| RA | 2,695,585 | (G)7→6 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 2,794,048 | T→C | intergenic (+33/‑205) | gabT → / → gabP | 4‑aminobutyrate aminotransferase GabT/4‑aminobutyrate:H(+) symporter |
| RA | 2,842,948 | A→G | G32G (GGT→GGC) | hycI ← | hydrogenase 3 maturation protease |
| RA | 2,876,096 | A→G | R78R (CGT→CGC) | cysD ← | sulfate adenylyltransferase subunit 2 |
| RA | 2,890,657 | G→A | G414G (GGC→GGT) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,918,003 | T→C | intergenic (+190/+42) | barA → / ← gudD | sensory histidine kinase BarA/D‑glucarate dehydratase |
| RA | 3,040,839 | T→C | T78A (ACA→GCA) | sdhE ← | FAD assembly factor |
| RA | 3,100,491 | A→G | S80P (TCC→CCC) | ansB ← | L‑asparaginase 2 |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,103,925 | T→C | W305R (TGG→CGG) | mutY → | adenine DNA glycosylase |
| RA | 3,204,663 | T→C | intergenic (‑74/‑31) | folB ← / → plsY | dihydroneopterin aldolase/putative glycerol‑3‑phosphate acyltransferase |
| RA | 3,218,808 | C→T | G90D (GGT→GAT) | aer ← | aerotaxis sensor receptor, flavoprotein |
| RA | 3,241,426 | T→C | T107A (ACC→GCC) | ygjV ← | inner membrane protein |
| RA | 3,365,444 | G→A | pseudogene (260/371 nt) | yhcE → | putative uncharacterized protein YhcE |
| RA | 3,383,151 | A→G | T318A (ACG→GCG) | degS → | serine endoprotease |
| RA | 3,393,031 | T→C | I1076M (ATA→ATG) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,475,341 | T→C | V126V (GTA→GTG) | tusD ← | sulfurtransferase complex subunit TusD |
| RA | 3,496,379 | T→C | V790A (GTA→GCA) | nirB → | nitrite reductase catalytic subunit NirB |
| RA | 3,500,813 | T→C | Y302H (TAC→CAC) | frlA → | fructoselysine/psicoselysine transporter |
| RA | 3,511,776 | C→T | R190H (CGT→CAT) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,627,172 | T→C | V789V (GTA→GTG) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,701,329 | T→A | I256N (ATC→AAC) | yhjV → | putative transporter YhjV |
| RA | 3,749,706 | T→C | F159L (TTT→CTT) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,806,353 | G→A | P239S (CCG→TCG) | waaG ← | lipopolysaccharide glucosyltransferase I |
| RA | 3,820,713 | T→C | D153G (GAC→GGC) | ligB ← | DNA ligase B |
| RA | 3,923,718 | G→A | intergenic (‑38/+26) | rsmG ← / ← mnmG | 16S rRNA m(7)G527 methyltransferase/5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,982,684 | (C)8→11 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,031,335 | T→C | W59R (TGG→CGG) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,058,912 | A→G | N169S (AAC→AGC) | bipA → | ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,063,931 | A→G | V122A (GTA→GCA) | ompL ← | putative outer membrane porin L |
| RA | 4,083,355 | A→G | V823A (GTC→GCC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,152,085 | T→C | E338E (GAA→GAG) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,367,959 | A→G | G123G (GGT→GGC) | aspA ← | aspartate ammonia‑lyase |
| RA | 4,377,308 | A→G | W139R (TGG→CGG) | blc ← | outer membrane lipoprotein Blc |
| RA | 4,472,426 | (A)8→7 | coding (108/135 nt) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,502,639 | A→G | W265R (TGG→CGG) | insG ← | KpLE2 phage‑like element; IS4 putative transposase |
| RA | 4,521,565 | (A)6→7 | coding (456/1350 nt) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,536,077 | Δ1 bp | intergenic (+46/+537) | yjhR → / ← nanS | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR/N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,549,394 | A→G | Y196C (TAC→TGC) | fimH → | type 1 fimbriae D‑mannose specific adhesin |
| RA | 4,556,797 | A→G | *48W (TGA→TGG) | ytiD → | protein YtiD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361208 | 361927 | 720 | 199 [192] | [195] 199 | lacA–[lacY] | lacA,[lacY] |
| * | * | ÷ | NC_000913 | 1870230 | 1873030 | 2801 | 356 [0] | [0] 344 | [yeaH]–[dgcJ] | [yeaH],cdgI,[dgcJ] |
| * | * | ÷ | NC_000913 | 2856995 | 2857095 | 101 | 199 [194] | [0] 306 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423679–3424234 | 3424613–3424238 | 5–935 | 198 [195] | [196] 198 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 316 (0.980) | 290 (0.930) | 138/188 | 0.7 | 65.5% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 338 (1.050) | 162/194 | 0.0 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1873031 = | 0 (0.000) | coding (991/1491 nt) | dgcJ | putative diguanylate cyclase DgcJ | |||||
| * | ? | NC_000913 | = 1870229 | 0 (0.000) | 354 (1.100) | 164/194 | 0.0 | 100% | coding (1275/1284 nt) | yeaH | DUF444 domain‑containing protein YeaH |
| ? | NC_000913 | 1978503 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||