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 | 170,793 | T→G | 14.6% | K476N (AAA→AAC) | fumB ← | class I fumarate hydratase |
| RA | NZ_CP022686 | 246,371 | T→G | 7.5% | N535T (AAC→ACC) | ydiJ ← | FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
| RA | NZ_CP022686 | 340,507 | G→C | 8.4% | L34V (CTT→GTT) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 340,511 | G→C | 8.2% | G32G (GGC→GGG) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 360,227 | T→G | 14.8% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 360,290 | T→G | 9.5% | T14P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 531,408 | A→C | 12.7% | K44N (AAA→AAC) | fliF → | flagellar basal‑body MS‑ring/collar protein FliF |
| RA | NZ_CP022686 | 556,949 | G→T | 15.6% | intergenic (+133/‑715) | 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 | 585,420 | A→C | 14.6% | W586G (TGG→GGG) | ybtQ ← | yersiniabactin ABC transporter ATP‑binding/permease protein YbtQ |
| RA | NZ_CP022686 | 601,302 | T→G | 25.6% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 687,661 | A→C | 7.5% | G107G (GGT→GGG) | CIW80_RS03525 ← | ParB N‑terminal domain‑containing protein |
| RA | NZ_CP022686 | 693,021 | A→C | 9.2% | T121P (ACG→CCG) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 694,406 | G→T | 13.3% | intergenic (+166/‑30) | 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 | 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 | 829,467 | C→A | 20.3% | intergenic (‑56/+171) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 881,733 | A→C | 17.4% | intergenic (+248/+139) | yohP → / ← dusC | protein YohP/tRNA dihydrouridine(16) synthase DusC |
| RA | NZ_CP022686 | 881,760 | T→G | 15.4% | 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 | 948,046 | G→T | 19.5% | intergenic (+115/‑142) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 948,049 | A→T | 10.8% | intergenic (+118/‑139) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 948,051 | G→T | 10.7% | intergenic (+120/‑137) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 1,005,085 | C→A | 11.9% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,034,493 | T→G | 8.7% | T26P (ACC→CCC) | menC ← | o‑succinylbenzoate synthase |
| RA | NZ_CP022686 | 1,174,279 | A→T | 9.8% | intergenic (+8/‑36) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 14.0% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,333,565 | C→A | 7.3% | L27F (TTG→TTT) | yfhb ← | phosphatidylglycerophosphatase C |
| RA | NZ_CP022686 | 1,360,709 | T→G | 10.0% | intergenic (‑44/+280) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,479,595 | G→C | 7.4% | intergenic (‑4/+189) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,479,633 | A→C | 11.0% | intergenic (‑42/+151) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,481,375 | A→C | 8.6% | V272G (GTG→GGG) | cysN ← | sulfate adenylyltransferase subunit CysN |
| RA | NZ_CP022686 | 1,504,257 | A→T | 15.7% | S232C (AGT→TGT) ‡ | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,258 | G→T | 14.7% | S232I (AGT→ATT) ‡ | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,289 | T→G | 15.9% | R242R (CGT→CGG) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,328 | G→T | 18.5% | M255I (ATG→ATT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,339 | C→A | 23.2% | P259Q (CCA→CAA) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,354 | C→A | 14.7% | A264D (GCT→GAT) ‡ | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,355 | T→A | 12.8% | A264A (GCT→GCA) ‡ | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,504,361 | G→T | 26.3% | V266V (GTG→GTT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,535,318 | A→T | 16.3% | M20L (ATG→TTG) | fucI → | L‑fucose isomerase |
| RA | NZ_CP022686 | 1,633,846 | T→G | 33.7% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,633,880 | T→G | 16.5% | S242R (AGC→CGC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,633,901 | T→G | 12.2% | T235P (ACG→CCG) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 11.5% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 8.9% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,716,145 | A→C | 9.0% | T42P (ACC→CCC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,758,771 | T→G | 6.8% | intergenic (+18/‑254) | sat → / → CIW80_RS08700 | serine protease autotransporter toxin Sat/transposase |
| RA | NZ_CP022686 | 1,775,845 | T→G | 7.8% | N198T (AAC→ACC) | CIW80_RS08815 ← | N‑acetylneuraminate epimerase |
| RA | NZ_CP022686 | 1,805,002 | C→A | 7.3% | pseudogene (283/934 nt) | CIW80_RS09020 → | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
| RA | NZ_CP022686 | 1,828,110 | A→C | 10.3% | R85R (CGT→CGG) | gspK ← | type II secretion system minor pseudopilin GspK |
| RA | NZ_CP022686 | 1,865,103 | A→C | 8.5% | L491V (TTG→GTG) | pitB ← | inorganic phosphate transporter PitB |
| RA | NZ_CP022686 | 1,954,923 | T→G | 15.5% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,016,225 | T→G | 9.9% | noncoding (49/377 nt) | rnpB ← | RNase P RNA component class A |
| RA | NZ_CP022686 | 2,047,984 | A→C | 8.4% | R624R (CGT→CGG) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,061,780 | A→C | 8.3% | K383N (AAA→AAC) | argG → | argininosuccinate synthase |
| RA | NZ_CP022686 | 2,061,804 | A→C | 12.7% | K391N (AAA→AAC) | argG → | argininosuccinate synthase |
| RA | NZ_CP022686 | 2,110,465 | T→G | 9.7% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 11.7% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,109 | T→G | 13.4% | V124G (GTG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,159,652 | A→C | 11.2% | N160T (AAC→ACC) | CIW80_RS10780 → | amino acid ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,172,177 | A→C | 6.8% | 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 | 2,272,284 | G→C | 6.5% | M1M (ATG→ATC) † | greB → | transcription elongation factor GreB |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,357,324 | A→C | 19.2% | N37T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,361,489 | T→G | 12.1% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,362,607 | T→G | 7.9% | L36R (CTT→CGT) | nikB → | nickel ABC transporter permease subunit NikB |
| RA | NZ_CP022686 | 2,394,287 | T→G | 22.1% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,394,302 | A→T | 11.5% | F110Y (TTC→TAC) | 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 |
| RA | NZ_CP022686 | 2,470,422 | T→G | 20.4% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,546,408 | C→A | 10.8% | M90I (ATG→ATT) | waaG ← | glycosyltransferase family 4 protein |
| RA | NZ_CP022686 | 2,546,423 | A→C | 14.0% | V85V (GTT→GTG) | waaG ← | glycosyltransferase family 4 protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,638,855 | C→A | 8.2% | intergenic (‑170/+70) | yidB ← / ← gyrB | YidB family protein/DNA topoisomerase (ATP‑hydrolyzing) subunit B |
| RA | NZ_CP022686 | 2,736,585 | T→A | 10.2% | Y183N (TAC→AAC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,755,007 | G→T | 8.8% | intergenic (‑20/+28) | cyaY ← / ← CIW80_RS13805 | iron donor protein CyaY/hypothetical protein |
| RA | NZ_CP022686 | 2,769,196 | A→C | 20.5% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,799,520 | A→C | 11.3% | G76G (GGT→GGG) | CIW80_RS14015 ← | tripartite tricarboxylate transporter permease |
| RA | NZ_CP022686 | 2,834,886 | A→C | 10.9% | K597N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 28.1% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 15.6% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,856 | T→G | 8.8% | K237N (AAA→AAC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 3,163,655 | T→G | 7.2% | V300G (GTC→GGC) | melA → | alpha‑galactosidase |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| 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 | 21.5% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,495,072 | A→C | 7.0% | Q161H (CAA→CAC) | yjtD → | tRNA/rRNA methyltransferase |
| RA | NZ_CP022686 | 3,652,079 | T→G | 13.3% | intergenic (‑88/+24) | panB ← / ← CIW80_RS18255 | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin |
| RA | NZ_CP022686 | 3,655,493 | G→T | 5.4% | I780I (ATC→ATA) | htrE ← | outer membrane usher protein |
| 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 | 20.7% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,734,380 | T→G | 19.5% | L229R (CTC→CGC) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,734,402 | T→G | 7.7% | G236G (GGT→GGG) | 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 | 3,797,493 | G→T | 14.1% | G134C (GGT→TGT) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,868,846 | T→G | 12.9% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,928,369 | T→G | 12.8% | W285G (TGG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 14.6% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,940,707 | A→C | 9.4% | F314V (TTT→GTT) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,940,724 | A→C | 11.0% | V308G (GTA→GGA) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 4,074,879 | G→T | 8.5% | L31M (CTG→ATG) | CIW80_RS20380 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,133,839 | T→G | 18.3% | K117T (AAA→ACA) | ybdF ← | MmcQ/YjbR family DNA‑binding protein |
| RA | NZ_CP022686 | 4,133,850 | T→G | 14.0% | K113N (AAA→AAC) | ybdF ← | MmcQ/YjbR family DNA‑binding protein |
| RA | NZ_CP022686 | 4,214,132 | A→T | 9.1% | intergenic (‑32/+6) | CIW80_RS21080 ← / ← CIW80_RS21085 | tRNA‑Gln/tRNA‑Gln |
| RA | NZ_CP022686 | 4,290,635 | T→G | 9.4% | T109P (ACC→CCC) | ybgS ← | YbgS‑like family protein |
| RA | NZ_CP022686 | 4,440,334 | A→C | 17.2% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,605,579 | T→G | 15.2% | T56P (ACG→CCG) | CIW80_RS23010 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 10.6% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,951 | A→C | 10.3% | N732T (AAC→ACC) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,762,516 | T→G | 14.9% | K368N (AAA→AAC) | mfd ← | transcription‑repair coupling factor |
| RA | NZ_CP022686 | 4,764,877 | T→G | 12.0% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,815,879 | T→G | 12.5% | F23V (TTC→GTC) | CIW80_RS24305 → | C40 family peptidase |
| 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 | 4,951,536 | G→C | 13.9% | A44P (GCC→CCC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,000,015 | T→G | 5.7% | F156V (TTT→GTT) | CIW80_RS25310 → | ABC transporter ATP‑binding protein |
| RA | NZ_CP022686 | 5,042,304 | T→C | 7.0% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 372–2618 | 3065–2957 | 340–2694 | 5970 [5937] | [5894] 6111 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2771–2840 | 5510–3245 | 406–2740 | 4232 [3924] | [3634] 4481 | 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 | 937548 = | 143 (0.840) | 10 (0.060) | 9/234 | NT | 6.6% | noncoding (63/77 nt) | CIW80_RS04765 | tRNA‑Pro |
| ? | NZ_CP022686 | = 949035 | 151 (0.950) | intergenic (+566/+139) | CIW80_RS04860/CIW80_RS26000 | hypothetical protein/autotransporter outer membrane beta‑barrel domain‑containing protein | |||||
| * | ? | NZ_CP022686 | 3322412 = | 137 (0.810) | 31 (0.180) | 19/250 | NT | 18.5% | coding (1690/1911 nt) | CIW80_RS16525 | site‑specific integrase |
| ? | NZ_CP022686 | 3369610 = | NA (NA) | intergenic (‑3/+8) | CIW80_RS16840/CIW80_RS16845 | restriction endonuclease/IS3‑like element ISEc52 family transposase | |||||
| * | ? | NZ_CP022686 | = 3322414 | 144 (0.850) | 21 (0.120) | 14/250 | NT | 12.7% | coding (1692/1911 nt) | CIW80_RS16525 | site‑specific integrase |
| ? | NZ_CP022686 | = 3395240 | NA (NA) | pseudogene (10/1107 nt) | yjhR | helicase YjhR | |||||