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 | 196,840 | A→C | 8.3% | N132T (AAC→ACC) | dtpA → | dipeptide/tripeptide permease DtpA |
| RA | NZ_CP022686 | 298,027 | A→C | 12.4% | F60C (TTT→TGT) | chbC ← | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
| RA | NZ_CP022686 | 418,374 | T→G | 11.8% | 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 | 473,113 | T→G | 7.5% | intergenic (+155/+10) | cmoB → / ← torZ | tRNA 5‑methoxyuridine(34)/uridine 5‑oxyacetic acid(34) synthase CmoB/trimethylamine N‑oxide reductase TorZ |
| 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 | 11.5% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 24.5% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,343 | A→G | 6.4% | D1623G (GAC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 687,661 | A→C | 8.6% | G107G (GGT→GGG) | CIW80_RS03525 ← | ParB N‑terminal domain‑containing protein |
| RA | NZ_CP022686 | 693,021 | A→C | 10.9% | T121P (ACG→CCG) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 694,391 | C→A | 12.3% | intergenic (+151/‑45) | CIW80_RS03555 → / → CIW80_RS03560 | transposase/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 | 829,441 | C→A | 23.1% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 19.0% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 881,760 | T→G | 20.8% | 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 | 948,049 | A→T | 13.1% | intergenic (+118/‑139) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 948,080 | G→T | 17.4% | intergenic (+149/‑108) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 948,090 | C→A | 19.8% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 1,000,439 | T→G | 26.3% | P942P (CCA→CCC) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,005,085 | C→A | 14.0% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,047,883 | T→G | 8.3% | intergenic (‑113/+51) | nuoM ← / ← nuoL | NADH‑quinone oxidoreductase subunit M/NADH‑quinone oxidoreductase subunit L |
| RA | NZ_CP022686 | 1,209,908 | T→G | 15.7% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,280,117 | T→G | 10.4% | N8H (AAC→CAC) | yfgM ← | ancillary SecYEG translocon subunit YfgM |
| RA | NZ_CP022686 | 1,370,556 | T→G | 12.7% | P99P (CCA→CCC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,371,071 | G→T | 18.9% | D29Y (GAT→TAT) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,504,250 | T→G | 15.3% | V229V (GTT→GTG) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,547,113 | G→C | 18.5% | intergenic (+25/‑9) | CIW80_RS07710 → / → CIW80_RS07715 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,558,395 | A→C | 15.3% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,564,589 | A→C | 9.7% | N197T (AAC→ACC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 16.9% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,640,925 | A→C | 13.4% | R7S (AGA→AGC) | ygfM → | molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,244 | T→G | 18.5% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 12.0% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,690,283 | T→G | 6.4% | L133V (TTA→GTA) | CIW80_RS08315 → | energy‑coupling factor transporter transmembrane component T |
| RA | NZ_CP022686 | 1,705,984 | T→G | 14.3% | intergenic (‑594/‑61) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,706,025 | C→A | 12.6% | intergenic (‑635/‑20) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,829,617 | A→C | 7.8% | V93G (GTT→GGT) | gspH ← | type II secretion system minor pseudopilin GspH |
| RA | NZ_CP022686 | 1,860,070 | C→A | 17.0% | E119* (GAA→TAA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,964,332 | A→C | 7.5% | G27G (GGT→GGG) | mug ← | G/U mismatch‑specific DNA glycosylase |
| RA | NZ_CP022686 | 1,965,173 | A→C | 13.3% | R86R (CGT→CGG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 1,974,549 | T→G | 7.8% | V986G (GTC→GGC) | ebgA → | beta‑galactosidase subunit alpha |
| RA | NZ_CP022686 | 2,056,143 | A→C | 8.9% | S623A (TCC→GCC) | infB ← | translation initiation factor IF‑2 |
| RA | NZ_CP022686 | 2,061,804 | A→C | 8.2% | K391N (AAA→AAC) | argG → | argininosuccinate synthase |
| RA | NZ_CP022686 | 2,110,465 | T→G | 9.5% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 9.9% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,115 | T→G | 11.7% | L126R (CTG→CGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,141 | T→G | 10.2% | F135V (TTC→GTC) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 8.1% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| 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 | 2,380,922 | A→C | 9.4% | S182R (AGC→CGC) | pitA → | inorganic phosphate transporter PitA |
| RA | NZ_CP022686 | 2,386,387 | C→A | 6.8% | G454C (GGT→TGT) | prlC ← | oligopeptidase A |
| RA | NZ_CP022686 | 2,393,013 | T→G | 6.8% | intergenic (+151/‑2) | slp → / → dctR | outer membrane lipoprotein Slp/LuxR C‑terminal‑related transcriptional regulator |
| RA | NZ_CP022686 | 2,394,287 | T→G | 19.4% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,397,370 | T→G | 9.3% | F9C (TTT→TGT) | chuT → | heme ABC transporter substrate‑binding protein ChuT |
| RA | NZ_CP022686 | 2,398,896 | A→C | 15.2% | K206N (AAA→AAC) | hutW → | heme anaerobic degradation radical SAM methyltransferase ChuW/HutW |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,460,576 | C→A | 11.0% | M1M (ATG→ATT) † | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,470,422 | T→G | 10.5% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,521,024 | T→G | 8.0% | V229G (GTT→GGT) | lldP → | L‑lactate permease |
| RA | NZ_CP022686 | 2,572,705 | A→C | 11.0% | G191G (GGT→GGG) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,429 | T→G | 10.7% | N230T (AAC→ACC) | CIW80_RS12895 ← | class II fructose‑bisphosphate aldolase family protein |
| RA | NZ_CP022686 | 2,574,451 | T→G | 10.8% | T223P (ACT→CCT) | 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 | 2,719,163 | T→G | 10.9% | K123N (AAA→AAC) | ilvY ← | HTH‑type transcriptional activator IlvY |
| RA | NZ_CP022686 | 2,769,196 | A→C | 11.7% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,801,852 | T→G | 5.5% | K20N (AAA→AAC) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 30.4% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 17.3% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,937,268 | G→T | 9.2% | P199Q (CCA→CAA) | yijO ← | AraC family transcriptional regulator |
| RA | NZ_CP022686 | 2,961,318 | A→C | 7.9% | intergenic (+96/‑277) | murI → / → CIW80_RS14765 | glutamate racemase/16S ribosomal RNA |
| RA | NZ_CP022686 | 3,017,611 | A→C | 6.2% | T836P (ACC→CCC) | metH → | methionine synthase |
| RA | NZ_CP022686 | 3,017,622 | A→C | 16.1% | K839N (AAA→AAC) | metH → | methionine synthase |
| RA | NZ_CP022686 | 3,136,940 | T→G | 13.7% | D161A (GAC→GCC) | phnN ← | ribose 1,5‑bisphosphokinase |
| RA | NZ_CP022686 | 3,136,948 | G→T | 13.2% | L158L (CTC→CTA) | 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 | 3,200,595 | A→C | 5.9% | V199G (GTT→GGT) | frdA ← | fumarate reductase (quinol) flavoprotein subunit |
| RA | NZ_CP022686 | 3,348,357 | T→G | 11.5% | intergenic (‑173/‑27) | CIW80_RS16685 ← / → CIW80_RS26495 | inovirus Gp2 family protein/hypothetical protein |
| RA | NZ_CP022686 | 3,390,616 | C→G | 14.0% | A143P (GCC→CCC) | sgcX ← | M42 family metallopeptidase |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,229 | T→G | 19.5% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,687,920 | T→G | 7.7% | D729A (GAC→GCC) | glnD ← | bifunctional uridylyltransferase/uridylyl‑removing protein GlnD |
| RA | NZ_CP022686 | 3,770,508 | T→G | 12.5% | intergenic (‑244/+219) | CIW80_RS26265 ← / ← CIW80_RS18890 | ATP‑binding protein/hypothetical protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,797,481 | T→G | 20.2% | L130V (TTA→GTA) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,806,256 | G→T | 17.4% | E1583* (GAA→TAA) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,806,265 | T→A | 10.0% | Y1586N (TAC→AAC) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,852,489 | A→T | 7.1% | L168* (TTA→TAA) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,868,846 | T→G | 14.4% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,894,249 | T→G | 7.7% | R154R (CGT→CGG) | ykgG → | lactate utilization protein C |
| RA | NZ_CP022686 | 4,025,356 | T→G | 6.5% | N445T (AAC→ACC) | ybaE ← | SgrR family transcriptional regulator |
| RA | NZ_CP022686 | 4,056,962 | C→A | 24.5% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,118,545 | G→T | 8.8% | S252* (TCA→TAA) | nfrA ← | bacteriophage adsorption protein NfrA |
| RA | NZ_CP022686 | 4,267,494 | C→T | 9.6% | G396G (GGC→GGT) | sdhA → | succinate dehydrogenase flavoprotein subunit |
| RA | NZ_CP022686 | 4,287,463 | T→A | 9.2% | noncoding (54/76 nt) | CIW80_RS21475 → | tRNA‑Val |
| RA | NZ_CP022686 | 4,290,635 | T→G | 5.4% | T109P (ACC→CCC) | ybgS ← | YbgS‑like family protein |
| RA | NZ_CP022686 | 4,331,905 | A→C | 11.1% | G300G (GGT→GGG) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,368,341 | T→G | 19.8% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,485,614 | T→G | 9.4% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,562,550 | T→G | 17.3% | N140H (AAC→CAC) | putA ← | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
| RA | NZ_CP022686 | 4,587,091 | T→G | 17.5% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,632,193 | T→G | 10.2% | L280R (CTT→CGT) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,951 | A→C | 12.1% | N732T (AAC→ACC) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,678,041 | A→C | 25.1% | intergenic (+39/‑82) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,678,047 | A→C | 27.0% | intergenic (+45/‑76) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,764,877 | T→G | 13.3% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,883 | A→T | 11.0% | intergenic (‑63/‑198) | 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 | 5,043,942 | C→G | 7.0% | V1191V (GTC→GTG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pHH‑29_RBS | 720 | A→C | 5.1% | intergenic (–/‑716) | – / → ompA | –/– |
| RA | pHH‑29_RBS | 1,587 | C→A | 11.6% | S30* (TCA→TAA) | Aldafermin (NGM282) → | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 394–2618 | 3049–2957 | 340–2656 | 7687 [7477] | [7419] 7620 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2769–2841 | 5512–3245 | 405–2744 | 6822 [6477] | [6207] 6880 | putative HTH domain protein (MarR‑like)–hypothetical protein | putative HTH domain protein (MarR‑like),putative HTH domain protein,uncharacterized protein,hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 730871 = | NA (NA) | 67 (0.450) | 39/244 | NT | 42.3% | intergenic (‑29/+28) | sbmC/CIW80_RS03815 | DNA gyrase inhibitor SbmC/ISL3‑like element ISEc53 family transposase |
| ? | NZ_CP022686 | 1821844 = | 93 (0.610) | coding (341/717 nt) | CIW80_RS09080 | K5 polysaccharide biosynthesis alpha‑UDP‑GlcNAc glycosyltransferase KfiA | |||||
| * | ? | NZ_CP022686 | = 732755 | NA (NA) | 75 (0.500) | 40/248 | NT | 47.8% | intergenic (‑99/+99) | CIW80_RS03820/dacD | ClbS/DfsB family four‑helix bundle protein/serine‑type D‑Ala‑D‑Ala carboxypeptidase DacD |
| ? | NZ_CP022686 | = 1821851 | 82 (0.540) | coding (334/717 nt) | CIW80_RS09080 | K5 polysaccharide biosynthesis alpha‑UDP‑GlcNAc glycosyltransferase KfiA | |||||