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 | seq id | position | mutation | freq | annotation | gene | description |
| RA | NZ_CP022686 | 77,247 | C→A | 5.5% | E135* (GAA→TAA) | digH ← | glycoside hydrolase family 10 protein |
| RA | NZ_CP022686 | 119,184 | T→G | 11.3% | F47V (TTT→GTT) | marB → | multiple antibiotic resistance protein MarB |
| RA | NZ_CP022686 | 340,516 | A→C | 8.5% | F31V (TTT→GTT) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 418,374 | T→G | 10.0% | F48V (TTT→GTT) | znuB → | zinc ABC transporter permease subunit ZnuB |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 482,315 | T→G | 11.1% | K183N (AAA→AAC) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | NZ_CP022686 | 496,135 | A→C | 15.2% | V382V (GTT→GTG) | otsA ← | alpha,alpha‑trehalose‑phosphate synthase |
| RA | NZ_CP022686 | 556,940 | A→T | 16.6% | intergenic (+124/‑724) | zinT → / → CIW80_RS03080 | metal‑binding protein ZinT/site‑specific integrase |
| RA | NZ_CP022686 | 560,880 | C→T | 100% | intergenic (+62/+53) | CIW80_RS03085 → / ← pilV | hypothetical protein/shufflon system plasmid conjugative transfer pilus tip adhesin PilV |
| RA | NZ_CP022686 | 601,295 | T→G | 19.0% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 19.6% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 651,848 | A→C | 13.7% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 694,457 | G→T | 22.0% | E8* (GAA→TAA) | CIW80_RS03560 → | PfkB family carbohydrate kinase |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,452 | G→T | 15.6% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 20.8% | intergenic (‑56/+171) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 864,173 | T→G | 17.5% | intergenic (+39/+2) | yehR → / ← yehS | YehR family lipoprotein/DUF1456 family protein |
| RA | NZ_CP022686 | 881,733 | A→C | 25.7% | intergenic (+248/+139) | yohP → / ← dusC | protein YohP/tRNA dihydrouridine(16) synthase DusC |
| RA | NZ_CP022686 | 917,427:1 | +TT | 100% | intergenic (+130/‑91) | yeiP → / → yeiQ | elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein |
| RA | NZ_CP022686 | 948,090 | C→A | 16.6% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 957,112 | T→G | 11.2% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,000,431 | T→G | 22.1% | D945A (GAC→GCC) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,000,443 | T→G | 16.4% | D941A (GAC→GCC) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,005,085 | C→A | 16.4% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,100,944 | T→G | 16.7% | D187A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,280,117 | T→G | 8.4% | N8H (AAC→CAC) | yfgM ← | ancillary SecYEG translocon subunit YfgM |
| RA | NZ_CP022686 | 1,360,724 | G→T | 16.8% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,727 | A→T | 13.9% | intergenic (‑62/+262) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,729 | G→T | 12.4% | intergenic (‑64/+260) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,756 | C→A | 11.5% | intergenic (‑91/+233) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,370,559 | T→G | 19.8% | K98N (AAA→AAC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,479,602 | G→T | 12.8% | intergenic (‑11/+182) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,479,619 | T→A | 10.7% | intergenic (‑28/+165) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,504,289 | T→G | 14.4% | R242R (CGT→CGG) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,361 | G→T | 23.8% | V266V (GTG→GTT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,558,395 | A→C | 15.4% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,564,569 | A→C | 12.6% | K190N (AAA→AAC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,564,589 | A→C | 9.1% | N197T (AAC→ACC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,640,925 | A→C | 11.0% | R7S (AGA→AGC) | ygfM → | molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,244 | T→G | 11.9% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,954,923 | T→G | 16.0% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,056,168 | A→C | 9.2% | G614G (GGT→GGG) | infB ← | translation initiation factor IF‑2 |
| RA | NZ_CP022686 | 2,061,804 | A→C | 10.8% | K391N (AAA→AAC) | argG → | argininosuccinate synthase |
| RA | NZ_CP022686 | 2,130,829 | A→C | 8.2% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,136 | T→G | 12.1% | V133G (GTT→GGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,179,877 | C→G | 7.5% | K35N (AAG→AAC) | rplQ ← | 50S ribosomal protein L17 |
| RA | NZ_CP022686 | 2,185,050 | A→C | 8.4% | R54R (CGT→CGG) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,185,075 | A→C | 11.1% | V46G (GTT→GGT) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,361,489 | T→G | 15.1% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,422,101 | C→A | 5.0% | intergenic (+374/‑19) | yhjD → / → yhjE | inner membrane protein YhjD/MFS transporter |
| RA | NZ_CP022686 | 2,550,305 | T→G | 6.0% | K151N (AAA→AAC) | mutM ← | bifunctional DNA‑formamidopyrimidine glycosylase/DNA‑(apurinic or apyrimidinic site) lyase |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,643,652 | T→G | 9.6% | D433A (GAC→GCC) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | NZ_CP022686 | 2,643,657 | A→C | 10.9% | G431G (GGT→GGG) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | NZ_CP022686 | 2,736,585 | T→A | 10.4% | Y183N (TAC→AAC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,758,128 | A→C | 10.1% | K40N (AAA→AAC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,780,149 | T→G | 5.2% | V690G (GTC→GGC) | metE → | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
| RA | NZ_CP022686 | 2,821,644 | A→C | 8.4% | intergenic (+100/‑278) | hemG → / → CIW80_RS14130 | menaquinone‑dependent protoporphyrinogen IX dehydrogenase/16S ribosomal RNA |
| RA | NZ_CP022686 | 2,868,740 | T→G | 21.0% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,915 | T→G | 9.2% | T218P (ACC→CCC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 2,937,203 | T→G | 11.2% | T221P (ACG→CCG) | yijO ← | AraC family transcriptional regulator |
| RA | NZ_CP022686 | 2,981,612 | A→C | 10.5% | T567P (ACC→CCC) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | NZ_CP022686 | 2,989,627 | T→G | 10.3% | Q39H (CAA→CAC) | thiC ← | phosphomethylpyrimidine synthase ThiC |
| RA | NZ_CP022686 | 3,090,101 | A→C | 11.2% | V9G (GTT→GGT) | yjcB ← | YjcB family protein |
| RA | NZ_CP022686 | 3,126,973 | G→T | 5.2% | G361G (GGC→GGA) | yjcS ← | alkyl sulfatase YjcS |
| RA | NZ_CP022686 | 3,136,940 | T→G | 9.1% | D161A (GAC→GCC) | phnN ← | ribose 1,5‑bisphosphokinase |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,252,198 | C→A | 15.4% | E219* (GAA→TAA) | CIW80_RS16225 ← | enoyl‑CoA hydratase/isomerase family protein |
| RA | NZ_CP022686 | 3,387,616 | G→T | 6.8% | I231I (ATC→ATA) | sgcQ ← | BtpA family protein SgcQ |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,215 | A→T | 14.1% | intergenic (‑24/+11) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,221 | T→G | 18.0% | intergenic (‑30/+5) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 16.6% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,231 | C→G | 12.9% | noncoding (82/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,516,075 | T→G | 10.0% | V213G (GTG→GGG) | nhaA → | Na+/H+ antiporter NhaA |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,731,466 | T→C | 100% | intergenic (+20/‑35) | rrf → / → CIW80_RS18620 | 5S ribosomal RNA/tRNA‑Asp |
| RA | NZ_CP022686 | 3,731,470 | C→T | 100% | intergenic (+24/‑31) | rrf → / → CIW80_RS18620 | 5S ribosomal RNA/tRNA‑Asp |
| RA | NZ_CP022686 | 3,731,473 | Δ1 bp | 100% | intergenic (+27/‑28) | rrf → / → CIW80_RS18620 | 5S ribosomal RNA/tRNA‑Asp |
| RA | NZ_CP022686 | 3,734,367 | T→G | 21.8% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,806,256 | G→T | 15.4% | E1583* (GAA→TAA) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,806,266 | A→C | 12.1% | Y1586S (TAC→TCC) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,852,459 | T→G | 12.5% | N178T (AAC→ACC) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,868,846 | T→G | 12.5% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,940,707 | A→C | 9.5% | F314V (TTT→GTT) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 9.3% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 11.3% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,032,283 | T→A | 15.3% | R103R (CGT→CGA) | glnK → | P‑II family nitrogen regulator |
| RA | NZ_CP022686 | 4,056,962 | C→A | 19.9% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,214,114 | A→T | 12.0% | intergenic (‑14/+24) | CIW80_RS21080 ← / ← CIW80_RS21085 | tRNA‑Gln/tRNA‑Gln |
| RA | NZ_CP022686 | 4,272,679 | A→C | 9.8% | T170P (ACC→CCC) | odhB → | 2‑oxoglutarate dehydrogenase complex dihydrolipoyllysine‑residue succinyltransferase |
| RA | NZ_CP022686 | 4,287,463 | T→A | 8.0% | noncoding (54/76 nt) | CIW80_RS21475 → | tRNA‑Val |
| RA | NZ_CP022686 | 4,368,341 | T→G | 17.7% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,368,372 | T→G | 11.5% | S37R (AGC→CGC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,412,269 | A→C | 8.9% | F246V (TTT→GTT) | ybjT ← | SDR family oxidoreductase |
| RA | NZ_CP022686 | 4,435,749 | A→C | 9.0% | intergenic (‑66/+57) | cydD ← / ← trxB | cysteine/glutathione ABC transporter permease/ATP‑binding protein CydD/thioredoxin‑disulfide reductase |
| RA | NZ_CP022686 | 4,440,297 | T→A | 11.1% | V785D (GTT→GAT) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,334 | A→C | 15.9% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,632,182 | T→G | 7.3% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,678,041 | A→C | 27.1% | intergenic (+39/‑82) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,678,047 | A→C | 30.4% | intergenic (+45/‑76) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,759,441 | A→C | 6.2% | V197G (GTT→GGT) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | NZ_CP022686 | 4,764,880 | T→G | 10.8% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,904 | G→T | 12.1% | intergenic (‑84/‑177) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,914 | C→A | 14.1% | intergenic (‑94/‑167) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,809,441 | T→G | 10.1% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,870,912 | Δ1 bp | 100% | intergenic (‑108/‑120) | dhaK ← / → dhaR | dihydroxyacetone kinase subunit DhaK/dihydroxyacetone kinase operon transcriptional regulator DhaR |
| RA | NZ_CP022686 | 4,951,538 | C→A | 17.5% | A44A (GCC→GCA) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 4,980,895 | A→C | 10.6% | C101W (TGT→TGG) | sapD ← | peptide ABC transporter ATP‑binding protein SapD |
| RA | NZ_CP022686 | 5,042,181 | T→A | 5.6% | S604R (AGT→AGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 12.4% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,347 | A→G | 6.1% | N993S (AAT→AGT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,942 | C→G | 6.5% | V1191V (GTC→GTG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,149 | T→A | 10.8% | G1260G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pHH‑29_RBS | 2,899 | Δ1 bp | 100% | intergenic (‑478/+230) | mok CDS ← / ← putative HTH domain protein (MarR‑like) | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 368–2618 | 3068–2957 | 340–2701 | 4879 [4866] | [4779] 5300 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 3743172 = | 218 (1.400) | 15 (0.100) | 12/248 | NT | 6.8% | intergenic (+1/+253) | CIW80_RS18695/CIW80_RS18700 | IS66 family transposase/IS110‑like element ISEc45 family transposase |
| ? | NZ_CP022686 | = 3744618 | 194 (1.260) | intergenic (‑60/‑4) | CIW80_RS18700/CIW80_RS18705 | IS110‑like element ISEc45 family transposase/transposase | |||||