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 | 162,405 | T→G | 9.1% | F46V (TTT→GTT) | ydgH → | DUF1471 family protein YdgH |
| RA | NZ_CP022686 | 230,696 | T→G | 9.5% | T103P (ACG→CCG) | ydhW ← | YdhW family putative oxidoreductase system protein |
| RA | NZ_CP022686 | 298,027 | A→C | 10.4% | 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 | 601,302 | T→G | 20.9% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 692,721 | T→G | 12.4% | L21V (TTA→GTA) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 694,457 | G→T | 11.8% | 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 | 764,997 | T→G | 11.7% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,441 | C→A | 27.3% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 16.2% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,472 | G→T | 13.1% | intergenic (‑61/+166) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 857,274 | T→G | 9.6% | G78G (GGT→GGG) | yehL → | MoxR family ATPase |
| RA | NZ_CP022686 | 881,733 | A→C | 16.4% | intergenic (+248/+139) | yohP → / ← dusC | protein YohP/tRNA dihydrouridine(16) synthase DusC |
| RA | NZ_CP022686 | 881,760 | T→G | 18.8% | intergenic (+275/+112) | 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 | 931,010 | A→C | 6.2% | F9V (TTT→GTT) | bcr ← | multidrug efflux MFS transporter Bcr |
| RA | NZ_CP022686 | 948,046 | G→T | 15.5% | intergenic (+115/‑142) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 957,112 | T→G | 13.3% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,000,431 | T→G | 23.7% | D945A (GAC→GCC) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,005,085 | C→A | 10.4% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,047,887 | C→A | 9.2% | intergenic (‑117/+47) | nuoM ← / ← nuoL | NADH‑quinone oxidoreductase subunit M/NADH‑quinone oxidoreductase subunit L |
| RA | NZ_CP022686 | 1,171,408 | C→G | 7.8% | intergenic (‑26/+14) | CIW80_RS05830 ← / ← CIW80_RS05835 | tRNA‑Ala/tRNA‑Ala |
| RA | NZ_CP022686 | 1,174,272 | A→C | 14.3% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,360,724 | G→T | 6.5% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,371,071 | G→T | 17.9% | D29Y (GAT→TAT) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,396,420 | T→G | 7.5% | intergenic (+26/‑211) | gabT → / → gabP | 4‑aminobutyrate‑‑2‑oxoglutarate transaminase/GABA permease |
| RA | NZ_CP022686 | 1,424,363 | G→T | 11.6% | intergenic (‑59/+4) | CIW80_RS07085 ← / ← CIW80_RS07090 | tRNA‑Arg/tRNA‑Arg |
| RA | NZ_CP022686 | 1,447,199 | A→C | 8.7% | V35G (GTA→GGA) | hycI ← | hydrogenase maturation peptidase HycI |
| RA | NZ_CP022686 | 1,458,792 | G→T | 7.3% | E66* (GAA→TAA) | flhA → | formate hydrogenlyase transcriptional activator FlhA |
| RA | NZ_CP022686 | 1,547,113 | G→C | 20.5% | intergenic (+25/‑9) | CIW80_RS07710 → / → CIW80_RS07715 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,558,395 | A→C | 10.5% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,579,312 | A→C | 11.4% | V107V (GTT→GTG) | CIW80_RS07835 ← | PRD domain‑containing protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 11.1% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,674,224 | T→G | 16.8% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 14.9% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,911,602 | T→G | 8.3% | N224T (AAC→ACC) | CIW80_RS09520 ← | MurR/RpiR family transcriptional regulator |
| RA | NZ_CP022686 | 1,925,332 | A→C | 8.5% | N151T (AAC→ACC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,954,923 | T→G | 17.0% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,049,089 | T→G | 18.2% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,056,193 | A→C | 7.7% | V606G (GTT→GGT) | infB ← | translation initiation factor IF‑2 |
| RA | NZ_CP022686 | 2,070,812 | A→C | 7.9% | intergenic (‑104/‑145) | greA ← / → dacB | transcription elongation factor GreA/serine‑type D‑Ala‑D‑Ala carboxypeptidase |
| RA | NZ_CP022686 | 2,110,457 | T→G | 11.9% | K12N (AAA→AAC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 9.4% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,141 | T→G | 10.4% | F135V (TTC→GTC) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,159,687 | T→A | 10.1% | Y172N (TAC→AAC) | CIW80_RS10780 → | amino acid ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,185,071 | A→C | 11.8% | G47G (GGT→GGG) | 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 | 2,394,287 | T→G | 14.2% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,643,657 | A→C | 16.1% | G431G (GGT→GGG) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | NZ_CP022686 | 2,717,416 | T→G | 7.3% | L106R (CTG→CGG) | ilvA → | threonine ammonia‑lyase, biosynthetic |
| RA | NZ_CP022686 | 2,758,128 | A→C | 9.4% | K40N (AAA→AAC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,808,135 | C→A | 15.6% | P444T (CCT→ACT) | ubiB → | ubiquinone biosynthesis regulatory protein kinase UbiB |
| RA | NZ_CP022686 | 2,808,142 | T→G | 10.5% | L446R (CTG→CGG) | ubiB → | ubiquinone biosynthesis regulatory protein kinase UbiB |
| RA | NZ_CP022686 | 2,868,740 | T→G | 19.7% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,915 | T→G | 7.0% | T218P (ACC→CCC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 3,020,229 | T→G | 15.2% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,265,084 | T→G | 13.2% | N77T (AAC→ACC) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,348,357 | T→G | 9.2% | intergenic (‑173/‑27) | 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 |
| JC | NZ_CP022686 | 3,448,150 | Δ3 bp | 5.7% | coding (1483‑1485/1665 nt) | tsr → | methyl‑accepting chemotaxis protein |
| RA | NZ_CP022686 | 3,451,843 | G→C | 10.1% | E278Q (GAA→CAA) | lgoD → | L‑galactonate oxidoreductase |
| RA | NZ_CP022686 | 3,461,229 | T→G | 25.8% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,247 | A→C | 13.8% | noncoding (66/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,469,923 | T→G | 8.2% | E122D (GAA→GAC) | yjjW ← | YjjW family glycine radical enzyme activase |
| RA | NZ_CP022686 | 3,504,108 | T→G | 5.1% | V222G (GTT→GGT) | tal → | transaldolase |
| JC | NZ_CP022686 | 3,509,100 | Δ12 bp | 6.9% | coding (1567‑1578/1917 nt) | dnaK → | molecular chaperone DnaK |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,734,367 | T→G | 21.0% | 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 | 3,798,080 | T→G | 7.9% | R329R (CGT→CGG) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,806,265 | T→A | 13.3% | Y1586N (TAC→AAC) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,932,437 | T→G | 11.0% | N186H (AAC→CAC) | lacA ← | galactoside O‑acetyltransferase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 11.7% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 13.4% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,056,962 | C→A | 16.1% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,133,850 | T→G | 12.1% | K113N (AAA→AAC) | ybdF ← | MmcQ/YjbR family DNA‑binding protein |
| RA | NZ_CP022686 | 4,280,095 | T→G | 10.3% | G103G (GGT→GGG) | cydB → | cytochrome d ubiquinol oxidase subunit II |
| RA | NZ_CP022686 | 4,287,456 | T→G | 13.8% | noncoding (47/76 nt) | CIW80_RS21475 → | tRNA‑Val |
| RA | NZ_CP022686 | 4,290,599 | T→G | 8.2% | T121P (ACC→CCC) | ybgS ← | YbgS‑like family protein |
| RA | NZ_CP022686 | 4,368,341 | T→G | 16.4% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,412,274 | A→C | 8.9% | V244G (GTG→GGG) | ybjT ← | SDR family oxidoreductase |
| RA | NZ_CP022686 | 4,562,600 | T→G | 17.7% | Q123P (CAG→CCG) | putA ← | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
| RA | NZ_CP022686 | 4,587,091 | T→G | 14.9% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,632,182 | T→G | 8.9% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,764,877 | T→G | 15.8% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,880 | T→G | 10.2% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,783,343 | C→A | 10.9% | G29V (GGA→GTA) | mnmA ← | tRNA 2‑thiouridine(34) synthase MnmA |
| RA | NZ_CP022686 | 4,814,990 | T→G | 16.2% | F71V (TTT→GTT) | CIW80_RS24295 → | phage tail protein |
| RA | NZ_CP022686 | 4,855,518 | G→C | 8.5% | V137V (GTC→GTG) | cvrA ← | potassium/proton antiporter |
| 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 | 4,905,221 | T→G | 13.4% | L116R (CTT→CGT) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 4,909,248 | A→T | 8.2% | intergenic (‑14/+20) | CIW80_RS24840 ← / ← CIW80_RS24845 | tRNA‑Tyr/tRNA‑Tyr |
| RA | NZ_CP022686 | 5,042,145 | A→G | 7.2% | K592K (AAA→AAG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 10.7% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,648 | G→C | 10.2% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,855 | T→A | 13.7% | G1162G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,641 | C→T | 6.0% | N1424N (AAC→AAT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 2,031 | G→A | 100% | intergenic (‑235/‑1500) | putative rom (RNA I inhibition modulator protein) ← / → ompA | –/– |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,595 | Δ15 bp | 100% | [IL2wt no signal] | [IL2wt no signal] | |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,019 | +CAT | 7.7% | intergenic (+12/+37) | IL2wt no signal → / ← annotated as hok_sok locus | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 189–287 | 3085–2957 | 2671–2897 | 6608 [6091] | [6453] 6549 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMut‑Ompa‑D5‑IL2wt‑His6 | 4743–4810 | 5417–5214 | 405–675 | 3075 [3054] | [2872] 3309 | [putative HTH domain protein] | [putative HTH domain protein] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 3743172 = | 204 (1.320) | 11 (0.070) | 11/246 | NT | 5.2% | intergenic (+1/+253) | CIW80_RS18695/CIW80_RS18700 | IS66 family transposase/IS110‑like element ISEc45 family transposase |
| ? | NZ_CP022686 | = 3744618 | 196 (1.270) | intergenic (‑60/‑4) | CIW80_RS18700/CIW80_RS18705 | IS110‑like element ISEc45 family transposase/transposase | |||||
| * | ? | NZ_CP022686 | 3899666 = | 219 (1.410) | 9 (0.070) | 9/216 | NT | 5.2% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 137 (1.010) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 207 (1.330) | 11 (0.080) | 11/216 | NT | 6.5% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 137 (1.010) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | 4514374 = | 157 (1.010) | 10 (0.000) +AGCT |
8/240 | NT | 11.1% | coding (59/1053 nt) | ompA | porin OmpA |
| ? | pMut‑Ompa‑D5‑IL2wt‑His6 | 3609 = | 8 (0.000) | coding (1/399 nt) | IL2wt no signal | ||||||