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 | 170,839 | A→C | 6.3% | L461R (CTG→CGG) | fumB ← | class I fumarate hydratase |
| RA | NZ_CP022686 | 298,027 | A→C | 15.9% | F60C (TTT→TGT) | chbC ← | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| 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 | 596,637 | T→G | 11.7% | G54G (GGT→GGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 20.3% | 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 | 13.2% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| 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 | 917,427:1 | +TT | 100% | intergenic (+130/‑91) | yeiP → / → yeiQ | elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein |
| RA | NZ_CP022686 | 1,005,085 | C→A | 13.4% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,047,883 | T→G | 7.9% | intergenic (‑113/+51) | nuoM ← / ← nuoL | NADH‑quinone oxidoreductase subunit M/NADH‑quinone oxidoreductase subunit L |
| RA | NZ_CP022686 | 1,065,997 | A→C | 12.9% | A30A (GCT→GCG) | yfbS ← | SLC13 family permease |
| RA | NZ_CP022686 | 1,137,229 | A→C | 9.2% | R243R (CGT→CGG) | emrK ← | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| RA | NZ_CP022686 | 1,145,575 | C→A | 11.1% | E332* (GAA→TAA) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | NZ_CP022686 | 1,237,918 | C→A | 15.4% | C303F (TGC→TTC) | tmcA ← | tRNA cytosine(34) acetyltransferase TmcA |
| RA | NZ_CP022686 | 1,360,724 | G→T | 11.3% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,366,277 | T→G | 9.3% | intergenic (‑278/+164) | CIW80_RS06740 ← / ← clpB | 16S ribosomal RNA/ATP‑dependent chaperone ClpB |
| RA | NZ_CP022686 | 1,504,361 | G→T | 21.7% | V266V (GTG→GTT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,564,569 | A→C | 14.6% | K190N (AAA→AAC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,579,312 | A→C | 10.3% | V107V (GTT→GTG) | CIW80_RS07835 ← | PRD domain‑containing protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 12.2% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,674,224 | T→G | 16.1% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 14.0% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 15.3% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,032 | G→T | 13.8% | intergenic (‑642/‑13) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,833,745 | T→G | 20.9% | N468H (AAC→CAC) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,833,749 | G→T | 13.7% | V466V (GTC→GTA) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,860,077 | G→T | 18.8% | G116G (GGC→GGA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,911,602 | T→G | 11.6% | N224T (AAC→ACC) | CIW80_RS09520 ← | MurR/RpiR family transcriptional regulator |
| RA | NZ_CP022686 | 1,954,923 | T→G | 15.2% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,037,521 | A→C | 18.8% | T508P (ACC→CCC) | lpoA → | penicillin‑binding protein activator LpoA |
| RA | NZ_CP022686 | 2,049,089 | T→G | 16.0% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,097 | A→T | 14.5% | R253R (CGT→CGA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,076,552 | A→C | 12.0% | intergenic (+22/‑211) | ispB → / → sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB |
| RA | NZ_CP022686 | 2,076,554 | T→G | 14.6% | intergenic (+24/‑209) | ispB → / → sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB |
| RA | NZ_CP022686 | 2,110,461 | A→T | 7.5% | V11E (GTA→GAA) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,123,241 | A→C | 9.1% | F208V (TTT→GTT) | tldD ← | metalloprotease TldD |
| RA | NZ_CP022686 | 2,148,118 | C→G | 11.4% | A127G (GCG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,141 | T→G | 11.2% | F135V (TTC→GTC) | panF → | sodium/pantothenate symporter |
| 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 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,429,953 | A→C | 8.9% | R275R (CGT→CGG) | dctA ← | C4‑dicarboxylate transporter DctC |
| RA | NZ_CP022686 | 2,470,422 | T→G | 12.8% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,516,312 | T→G | 11.4% | G574G (GGT→GGG) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,516,638 | C→A | 10.8% | T683N (ACC→AAC) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,516,657 | C→A | 11.5% | A689A (GCC→GCA) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,572,721 | A→C | 11.4% | F186C (TTT→TGT) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,429 | T→G | 12.7% | N230T (AAC→ACC) | CIW80_RS12895 ← | class II fructose‑bisphosphate aldolase family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,717,385 | T→G | 7.9% | F96V (TTT→GTT) | ilvA → | threonine ammonia‑lyase, biosynthetic |
| RA | NZ_CP022686 | 2,736,585 | T→A | 13.3% | Y183N (TAC→AAC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,601 | G→T | 13.9% | intergenic (+16/‑27) | CIW80_RS13750 → / → CIW80_RS13755 | tRNA‑Leu/tRNA‑Pro |
| RA | NZ_CP022686 | 2,758,109 | A→C | 6.1% | N34T (AAC→ACC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,769,196 | A→C | 16.8% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,780,110 | T→G | 6.0% | F677C (TTT→TGT) | metE → | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
| RA | NZ_CP022686 | 2,793,267 | T→G | 6.6% | D412A (GAC→GCC) | fdrA ← | acyl‑CoA synthetase FdrA |
| RA | NZ_CP022686 | 2,868,740 | T→G | 19.8% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 14.9% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,871,422 | T→G | 8.1% | N149T (AAC→ACC) | fdnG ← | formate dehydrogenase‑N subunit alpha |
| RA | NZ_CP022686 | 2,920,385 | C→A | 7.8% | A54E (GCA→GAA) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 2,961,318 | A→C | 9.2% | intergenic (+96/‑277) | murI → / → CIW80_RS14765 | glutamate racemase/16S ribosomal RNA |
| RA | NZ_CP022686 | 3,020,229 | T→G | 12.2% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,136,923 | A→C | 10.3% | S167A (TCG→GCG) | phnN ← | ribose 1,5‑bisphosphokinase |
| RA | NZ_CP022686 | 3,136,940 | T→G | 14.9% | 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 | 3,348,345 | G→T | 9.9% | intergenic (‑161/‑39) | CIW80_RS16685 ← / → CIW80_RS26495 | inovirus Gp2 family protein/hypothetical protein |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,444,704 | T→G | 10.4% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,229 | T→G | 19.2% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,516,093 | T→G | 9.3% | V219G (GTG→GGG) | nhaA → | Na+/H+ antiporter NhaA |
| RA | NZ_CP022686 | 3,516,129 | T→G | 8.4% | V231G (GTC→GGC) | nhaA → | Na+/H+ antiporter NhaA |
| RA | NZ_CP022686 | 3,604,565 | A→T | 15.2% | intergenic (+81/‑150) | lpxC → / → secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/secA translation cis‑regulator SecM |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,868,846 | T→G | 13.5% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,869,697 | T→G | 7.3% | N99T (AAC→ACC) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,928,369 | T→G | 11.0% | W285G (TGG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,928,381 | C→G | 8.2% | H289D (CAT→GAT) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 10.3% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 4,056,962 | C→A | 15.8% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,061,214 | A→C | 9.7% | L432R (CTG→CGG) | ybaL ← | YbaL family putative K(+) efflux transporter |
| RA | NZ_CP022686 | 4,074,902 | G→T | 13.1% | S23* (TCG→TAG) | CIW80_RS20380 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,196,276 | T→G | 18.1% | E15D (GAA→GAC) | holA ← | DNA polymerase III subunit delta |
| RA | NZ_CP022686 | 4,214,235 | C→A | 8.4% | intergenic (‑23/+26) | CIW80_RS21085 ← / ← CIW80_RS21090 | tRNA‑Gln/tRNA‑Met |
| RA | NZ_CP022686 | 4,368,380 | T→G | 16.1% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,334 | A→C | 20.5% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,485,614 | T→G | 14.5% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,587,091 | T→G | 10.0% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,632,182 | T→G | 12.8% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,764,880 | T→G | 10.7% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| 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 | 4,980,895 | A→C | 9.1% | C101W (TGT→TGG) | sapD ← | peptide ABC transporter ATP‑binding protein SapD |
| RA | NZ_CP022686 | 5,042,073 | A→G | 7.9% | A568A (GCA→GCG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,347 | A→G | 7.0% | N993S (AAT→AGT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,648 | G→C | 6.2% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,879 | C→T | 6.6% | G1170G (GGC→GGT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 1,375 | Δ1 bp | 6.7% | intergenic (–/+342) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 1,376 | Δ1 bp | 100% | intergenic (–/+341) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 93.7% | intergenic (‑341/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,127 | C→A | 100% | intergenic (‑345/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,132 | 4 bp→TA | 100% | intergenic (‑350/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 189 | 3084–2957 | 2769–2896 | 9189 [8325] | [8320] 9082 | 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 | 3899666 = | 182 (1.210) | 20 (0.150) | 15/218 | NT | 12.1% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 132 (1.010) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 169 (1.120) | 20 (0.150) | 15/218 | NT | 12.5% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 132 (1.010) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 2978 (0.490) | 3937 (0.650) | 184/250 | NT | 65.2% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 1220 (0.200) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 4357 (0.720) | 3128 (0.650) | 146/200 | NT | 57.1% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 1221 (0.250) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||