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 | 10,641 | T→C | intergenic (‑147/+2) | satP ← / ← yaaW | acetate/succinate:H(+) symporter/putative enzyme‑specific chaperone YaaW |
| RA | 169,672 | G→A | G730D (GGC→GAC) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 185,089 | (A)7→8 | intergenic (‑20/+34) | yaeI ← / ← dapD | phosphodiesterase YaeI/tetrahydrodipicolinate succinylase |
| RA | 188,389 | C→T | A88T (GCA→ACA) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 301,344 | C→T | E182K (GAG→AAG) | paoB ← | aldehyde dehydrogenase, FAD‑binding subunit |
| RA | 311,430 | A→G | intergenic (‑94/‑682) | ecpR ← / → ykgL | DNA‑binding transcriptional dual regulator MatA/uncharacterized protein YkgL |
| RA | 366,162 | A→G | P48P (CCT→CCC) | lacZ ← | beta‑galactosidase |
| RA | 371,588 | (G)6→5 | coding (350/867 nt) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 385,965 | A→G | Q245R (CAG→CGG) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 422,084 | G→C | A367P (GCC→CCC) | proY → | putative transporter ProY |
| RA | 426,178 | T→C | R14R (CGT→CGC) | tgt → | tRNA‑guanine transglycosylase |
| RA | 474,678 | G→A | P162S (CCG→TCG) | tesB ← | acyl‑CoA thioesterase II |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 549,150 | T→A | I265N (ATT→AAT) | ylbE → | DUF1116 domain‑containing protein YlbE |
| RA | 685,477 | G→A | F151F (TTC→TTT) | gltK ← | glutamate/aspartate ABC transporter membrane subunit GltK |
| RA | 698,467 | A→G | G237G (GGT→GGC) | asnB ← | asparagine synthetase B |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,001,023 | (A)8→7 | coding (1808/2601 nt) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,142,837 | +GC | coding (1531/3186 nt) | rne ← | ribonuclease E |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,296,446 | T→C | Y559C (TAC→TGC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,532,756 | A→G | D314G (GAC→GGC) | ydcC → | H repeat‑associated putative transposase YdcC |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,635,293 | G→A | T185T (ACC→ACT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,296 | T→G | G184G (GGA→GGC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,322 | C→T | E176K (GAA→AAA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,335 | C→T | T171T (ACG→ACA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,470 | 2 bp→GG | coding (377‑378/963 nt) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,488 | T→A | A120A (GCA→GCT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,505 | T→C | T115A (ACT→GCT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,738,705 | A→G | T288A (ACC→GCC) | purR → | DNA‑binding transcriptional repressor PurR |
| RA | 1,803,116 | T→C | pseudogene (23/1900 nt) | arpB → | putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,838,357 | (G)5→4 | coding (1146/1536 nt) | ynjC → | putative ABC transporter membrane subunit YnjC |
| RA | 1,866,547 | (T)5→6 | intergenic (‑75/‑361) | mipA ← / → yeaG | scaffolding protein that interacts with murein polymerase and murein hydrolase/protein kinase YeaG |
| 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 | 1,935,978 | T→C | T113A (ACC→GCC) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| RA | 1,964,688 | G→A | G121G (GGC→GGT) | flhA ← | flagellar biosynthesis protein FlhA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,122,619 | T→C | T121A (ACC→GCC) | cpsG ← | phosphomannomutase |
| RA | 2,134,271 | T→C | E461G (GAA→GGA) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,301,060 | A→G | F565S (TTC→TCC) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,426,832 | T→C | intergenic (‑44/+177) | hisJ ← / ← argT | histidine ABC transporter periplasmic binding protein/lysine/arginine/ornithine ABC transporter periplasmic binding protein |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,481,956 | C→T | G74D (GGC→GAC) | emrY ← | tripartite efflux pump membrane subunit EmrY |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,528,483 | G→A | A565V (GCC→GTC) | ligA ← | DNA ligase |
| RA | 2,555,795 | G→A | N202N (AAC→AAT) | eutL ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,583,930 | A→G | L532L (CTT→CTC) | aegA ← | putative oxidoreductase Fe‑S subunit AegA |
| RA | 2,585,779 | (T)7→8 | coding (49/1701 nt) | narQ → | sensory histidine kinase NarQ |
| RA | 2,673,499 | C→T | P52S (CCA→TCA) | yphA → | putative inner membrane protein |
| RA | 2,732,693 | T→C | D494G (GAC→GGC) | clpB ← | ClpB chaperone |
| RA | 2,782,569 | C→T | R53Q (CGA→CAA) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,833,404 | T→C | V310A (GTC→GCC) | norV → | anaerobic nitric oxide reductase flavorubredoxin |
| RA | 2,840,022 | G→A | A167T (GCA→ACA) | ascF → | beta‑glucoside specific PTS enzyme IIBC component |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,880,582 | G→A | P156L (CCG→CTG) | casD ← | type I‑E CRISPR system Cascade subunit CasD |
| RA | 2,900,306 | (A)9→10 | intergenic (‑33/‑286) | ygcW ← / → yqcE | putative deoxygluconate dehydrogenase/putative transport protein YqcE |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,972,909 | (C)6→5 | coding (954/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 3,020,047 | G→A | G296D (GGC→GAC) | ssnA → | putative aminohydrolase |
| RA | 3,058,775 | T→C | N184S (AAC→AGC) | rpiA ← | ribose‑5‑phosphate isomerase A |
| RA | 3,063,580 | T→C | V198V (GTT→GTC) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,105,587 | A→G | intergenic (+75/‑127) | mltC → / → nupG | membrane‑bound lytic murein transglycosylase C/nucleoside:H(+) symporter NupG |
| RA | 3,123,941 | G→A | G97G (GGC→GGT) | glcG ← | putative heme‑binding protein GlcG |
| RA | 3,153,755 | (G)5→6 | coding (193/660 nt) | yghB → | DedA family protein YghB |
| RA | 3,203,390 | A→G | L248L (TTG→CTG) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,568,390 | T→C | L313L (TTA→TTG) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,688,510 | A→G | Y222H (TAC→CAC) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | 3,742,829 | T→C | F33L (TTC→CTC) | yiaK → | 2,3‑diketo‑L‑gulonate reductase |
| RA | 3,758,973 | C→T | V297I (GTT→ATT) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,760,826 | T→C | T142A (ACG→GCG) | selA ← | selenocysteine synthase |
| RA | 3,773,041 | (G)6→7 | coding (761/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,773,405 | C→T | S375S (AGC→AGT) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 4,004,479 | A→G | G73G (GGT→GGC) | yigI ← | putative thioesterase YigI |
| RA | 4,190,784 | A→G | V362A (GTA→GCA) | thiH ← | 2‑iminoacetate synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| MC | 4,326,086 | Δ100 bp | between other | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
| RA | 4,430,216 | A→G | D118G (GAC→GGC) | cycA → | serine/alanine/glycine/cycloserine:H(+)symporter |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,467,200 | A→G | V16A (GTG→GCG) | treR ← | DNA‑binding transcriptional repressor TreR |
| RA | 4,542,303 | A→G | E89E (GAA→GAG) | fimE → | regulator for fimA |
| RA | 4,565,114 | C→T | G246D (GGC→GAC) | yjiM ← | putative dehydratase subunit |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 271502–271585 | 271645–271587 | 3–144 | 11 [7] | [10] 12 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 1635352–1635371 | 1635462 | 92–111 | 13 [10] | [10] 11 | ydfN | Qin prophage; putative side tail fiber assembly protein |
| * | * | ÷ | NC_000913 | 3423783–3424233 | 3424542–3424239 | 7–760 | 11 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3941771–3942011 | 3943280–3942036 | 26–1510 | 12 [8] | [9] 11 | [rrsC] | [rrsC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 21 (0.610) | 10/190 | 1.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 14 (0.280) +T |
10/274 | 2.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375304 = | NA (NA) | 16 (0.380) | 10/232 | 2.3 | NA | noncoding (17/36 nt) | other | REP31h |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 19 (0.590) +48 bp |
9/180 | 1.8 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | 2347201 = | NA (NA) | intergenic (+51/‑183) | nrdA/nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta | |||||
| * | ? | NC_000913 | 1207790 = | 16 (0.320) | 50 (1.130) | 36/244 | 0.2 | 76.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 16 (0.360) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.320) | 27 (0.610) | 23/244 | 0.8 | 64.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.360) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 59 (1.220) | 38/268 | 0.2 | 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 = | 91 (1.820) | 70 (1.410) | 43/274 | 0.1 | 60.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 48 (0.960) | 36/276 | 0.3 | 96.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||