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 | 1,207 | C→T | P291S (CCA→TCA) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 57,230 | A→G | intergenic (‑121/‑134) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 161,822 | A→G | P70P (CCT→CCC) | thpR ← | RNA 2',3'‑cyclic phosphodiesterase |
| RA | 163,281 | T→C | L393L (TTA→CTA) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 185,507 | A→G | G147G (GGT→GGC) | dapD ← | tetrahydrodipicolinate succinylase |
| RA | 248,419 | A→G | pseudogene (1652/1713 nt) | lfhA ← | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 313,061 | A→G | intergenic (‑284/+80) | ykgM ← / ← ykgR | putative ribosomal protein/putative membrane protein YkgR |
| RA | 385,891 | C→T | V220V (GTC→GTT) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 407,822 | T→C | V132A (GTG→GCG) | aroM → | protein AroM |
| RA | 450,996 | A→G | G205G (GGT→GGC) | cyoA ← | cytochrome bo3 ubiquinol oxidase subunit 2 |
| RA | 502,665 | T→C | T192A (ACC→GCC) | ybaL ← | putative transporter YbaL |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| MC JC | 545,679 | (TCA)4→3 | coding (683‑685/1050 nt) | allD ← | ureidoglycolate dehydrogenase |
| RA | 571,064 | T→C | S58P (TCT→CCT) | ybcL → | DLP12 prophage; periplasmic protein YbcL |
| RA | 601,908 | A→G | intergenic (+51/‑51) | cusA → / → pheP | copper/silver export system RND permease/phenylalanine:H(+) symporter PheP |
| RA | 666,790 | A→G | G476G (GGT→GGC) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 675,636 | A→G | R304R (CGT→CGC) | ybeQ ← | Sel1 repeat‑containing protein YbeQ |
| RA | 813,081 | C→T | intergenic (+134/‑445) | bioD → / → uvrB | dethiobiotin synthetase/excision nuclease subunit B |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 899,749 | A→G | intergenic (+104/+95) | rlmC → / ← artJ | 23S rRNA m(5)U747 methyltransferase/L‑arginine ABC transporter periplasmic binding protein |
| RA | 906,132 | A→G | Y208H (TAT→CAT) | ybjS ← | putative NAD(P)H‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 955,315 | C→T | D440N (GAT→AAT) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 987,008 | (T)8→7 | intergenic (‑26/+577) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,026,812 | (C)6→7 | coding (204/459 nt) | mgsA ← | methylglyoxal synthase |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,152,953 | A→G | T339A (ACC→GCC) | fabF → | beta‑ketoacyl‑[acyl carrier protein] synthase II |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,225,935 | A→G | V49A (GTA→GCA) | minC ← | Z‑ring positioning protein MinC |
| RA | 1,247,832 | A→G | V428A (GTA→GCA) | dhaM ← | dihydroxyacetone kinase subunit M |
| RA | 1,417,580 | A→G | C62R (TGC→CGC) | racC ← | Rac prophage; protein RacC |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← ydbK | small regulatory RNA MicC/putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,486,271 | C→T | R1071C (CGC→TGC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,570,678 | A→G | G456G (GGT→GGC) | gadB ← | glutamate decarboxylase B |
| RA | 1,585,101 | (C)6→7 | coding (1386/2280 nt) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,366 | A→G | pseudogene (721/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,613,791 | T→C | N305D (AAC→GAC) | sad ← | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| RA | 1,619,256 | T→C | L46P (CTC→CCC) | marR → | DNA‑binding transcriptional repressor MarR |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,690,397 | T→C | A182A (GCT→GCC) | ydgA → | conserved protein YdgA |
| RA | 1,704,558 | G→A | R3H (CGT→CAT) | blr → | beta‑lactam resistance protein |
| RA | 1,705,638 | T→C | V130A (GTC→GCC) | ydgK → | conserved inner membrane protein YdgK |
| RA | 1,717,614 | T→C | S132G (AGC→GGC) | pdxH ← | pyridoxal 5‑phosphate synthase |
| RA | 1,720,785 | G→A | R14C (CGC→TGC) | slyA ← | DNA‑binding transcriptional dual regulator SlyA |
| RA | 1,845,130 | C→T | V611M (GTG→ATG) | topB ← | DNA topoisomerase III |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,884,521 | A→G | Y445C (TAC→TGC) | yeaV → | putative transporter YeaV |
| RA | 1,923,946 | (G)6→7 | coding (646/873 nt) | yebZ ← | putative inner membrane protein |
| RA | 1,954,295 | G→A | R285H (CGC→CAC) | cmoB → | tRNA U34 carboxymethyltransferase |
| RA | 1,957,269 | A→G | G288G (GGT→GGC) | torY ← | cytochrome c quinol dehydrogenase TorY |
| RA | 1,970,201 | T→C | T262A (ACG→GCG) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,106 | (C)6→8 | intergenic (‑147/‑116) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,021,330 | G→A | L81L (CTG→CTA) | fliN → | flagellar motor switch protein FliN |
| RA | 2,100,643 | T→C | N209S (AAC→AGC) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,102,890 | T→C | R8G (AGA→GGA) | insH‑7 ← | IS5 transposase and trans‑activator |
| RA | 2,124,560 | T→C | N396S (AAC→AGC) | wcaI ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,146,009 | A→G | D915G (GAT→GGT) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,199,072 | G→A | intergenic (+1774/‑1207) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,240,754 | (C)5→6 | coding (915/1041 nt) | galS ← | DNA‑binding transcriptional dual regulator GalS |
| RA | 2,304,469 | T→C | intergenic (+76/+639) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,569,455 | T→C | Q19Q (CAA→CAG) | eutG ← | putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,596,151 | T→C | N196S (AAC→AGC) | ypfJ ← | uncharacterized protein YpfJ |
| RA | 2,617,121 | C→T | A343V (GCA→GTA) | bepA → | beta‑barrel assembly‑enhancing protease |
| RA | 2,656,431 | G→A | intergenic (‑73/+105) | pepB ← / ← iscX | aminopeptidase B/accessory iron‑sulfur cluster assembly protein IscX |
| RA | 2,730,975 | A→G | noncoding (183/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 2,736,758 | T→C | Y205H (TAC→CAC) | bamD → | outer membrane protein assembly factor BamD |
| RA | 2,752,610 | A→G | E272E (GAA→GAG) | recN → | DNA repair protein RecN |
| RA | 2,756,161 | G→A | M1M (ATG→ATA) † | intA → | CP4‑57 prophage; integrase |
| RA | 2,769,648 | (C)6→7 | intergenic (+162/‑55) | yfjQ → / → yfjR | CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,772,546 | T→C | pseudogene (637/1016 nt) | yfjV ← | CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| RA | 2,779,116 | G→A | P1204L (CCA→CTA) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,827,053 | G→A | C221Y (TGT→TAT) | srlE → | sorbitol‑specific PTS enzyme IIBC1 component |
| RA | 2,836,487 | T→C | E313E (GAA→GAG) | hypF ← | carbamoyltransferase HypF |
| RA | 2,855,659 | T→C | M441T (ATG→ACG) | fhlA → | DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,911,907 | (T)6→7 | coding (1745/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,957,921 | T→C | T322A (ACA→GCA) | ptrA ← | protease 3 |
| RA | 2,971,378 | C→T | T36T (ACC→ACT) | ygdR → | DUF903 domain‑containing lipoprotein YgdR |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,216,837 | G→A | C20Y (TGC→TAC) | nfeR → | DNA‑binding transcriptional repressor NfeR |
| RA | 3,283,673 | T→C | G177G (GGT→GGC) | kbaY → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaY |
| RA | 3,296,870 | T→C | G154G (GGT→GGC) | yraP → | divisome‑associated lipoprotein YraP |
| RA | 3,348,548 | T→C | Y33H (TAC→CAC) | yrbL → | protein kinase‑like domain‑containing protein YrbL |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,386,758 | G→A | F477F (TTC→TTT) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,396,729 | T→C | H356R (CAC→CGC) | rng ← | RNase G |
| RA | 3,449,125 | G→A | G15G (GGC→GGT) | rplP ← | 50S ribosomal subunit protein L16 |
| RA | 3,463,649 | T→C | A242A (GCT→GCC) | gspK → | Type II secretion system protein GspK |
| RA | 3,520,593 | C→T | L37L (TTG→TTA) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,728,742 | A→G | G210G (GGT→GGC) | xylB ← | xylulokinase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,839,562 | A→G | G144G (GGT→GGC) | nlpA ← | lipoprotein‑28 |
| RA | 3,846,928 | Δ1 bp | coding (240/1392 nt) | uhpT ← | hexose‑6‑phosphate:phosphate antiporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,905,639 | (A)9→10 | intergenic (‑42/+92) | bglF ← / ← bglG | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase/transcriptional antiterminator BglG |
| RA | 3,927,906 | C→T | S251F (TCC→TTC) | asnA → | asparagine synthetase A |
| RA | 4,030,704 | +A | coding (268/2190 nt) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,079,836 | A→G | D29G (GAC→GGC) | yiiF → | protein YiiF |
| RA | 4,095,618 | G→A | A122V (GCG→GTG) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,146,746 | A→G | L163L (TTA→TTG) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,366,473 | A→G | F101L (TTT→CTT) | dcuA ← | C4‑dicarboxylate transporter DcuA |
| RA | 4,409,506 | C→T | R78C (CGT→TGT) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,415,898 | T→C | *542Q (TAA→CAA) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,513,886 | A→G | A141A (GCT→GCC) | fecB ← | ferric citrate ABC transporter periplasmic binding protein |
| RA | 4,533,547 | G→A | H80Y (CAC→TAC) | yjhQ ← | KpLE2 phage‑like element; putative acetyltransferase TopAI antitoxin YjhQ |
| RA | 4,584,837 | A→G | V642A (GTT→GCT) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| JC | 4,606,094 | (G)8→11 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423768–3424233 | 3424523–3424240 | 8–756 | 14 [13] | [7] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3945684–3945905 | 3946103–3945915 | 11–420 | 14 [12] | [10] 14 | rrlC | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3946329–3946619 | 3946827–3946697 | 79–499 | 14 [12] | [12] 16 | [rrlC]–rrfC | [rrlC],rrfC |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 79 (1.280) | 19 (0.350) | 15/244 | 2.0 | 24.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 47 (0.860) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 48 (0.800) | 34/268 | 0.6 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 92 (1.500) | 96 (1.570) | 51/274 | 0.1 | 67.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 83 (1.350) | 54/276 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 32 (0.520) | 16 (0.280) | 15/258 | 2.2 | 28.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 51 (0.890) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||