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 | 119,184 | T→G | 17.7% | F47V (TTT→GTT) | marB → | multiple antibiotic resistance protein MarB |
| RA | NZ_CP022686 | 238,317 | G→T | 23.2% | L88I (CTT→ATT) | sufE ← | cysteine desulfuration protein SufE |
| RA | NZ_CP022686 | 268,665 | T→C | 5.7% | intergenic (+68/‑64) | aroH → / → hemP | 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP |
| RA | NZ_CP022686 | 360,246 | T→G | 14.6% | E28D (GAA→GAC) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 372,574 | A→C | 21.6% | N275T (AAC→ACC) | sdaA → | L‑serine ammonia‑lyase |
| 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 | 601,295 | T→G | 15.0% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 22.8% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 636,692 | A→C | 5.7% | R459R (CGT→CGG) | clbM ← | precolibactin export MATE transporter ClbM |
| RA | NZ_CP022686 | 693,021 | A→C | 10.5% | T121P (ACG→CCG) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| 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 | 881,760 | T→G | 15.9% | 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 | 22.7% | intergenic (+115/‑142) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 957,112 | T→G | 13.5% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,100,959 | T→G | 15.7% | D182A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,169,059 | C→T | 5.4% | R681K (AGA→AAA) | pdeA ← | sensor domain‑containing phosphodiesterase |
| RA | NZ_CP022686 | 1,209,917 | G→T | 17.9% | P393Q (CCA→CAA) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,276,970 | A→C | 11.1% | G414G (GGT→GGG) | der ← | ribosome biogenesis GTPase Der |
| RA | NZ_CP022686 | 1,370,556 | T→G | 17.5% | P99P (CCA→CCC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,396,426 | T→G | 8.7% | intergenic (+32/‑205) | gabT → / → gabP | 4‑aminobutyrate‑‑2‑oxoglutarate transaminase/GABA permease |
| RA | NZ_CP022686 | 1,479,625 | G→C | 9.8% | intergenic (‑34/+159) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,547,000 | G→C | 14.9% | intergenic (+22/‑12) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,674,244 | T→G | 10.9% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 11.3% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,828,110 | A→C | 9.4% | R85R (CGT→CGG) | gspK ← | type II secretion system minor pseudopilin GspK |
| RA | NZ_CP022686 | 1,828,113 | A→C | 11.2% | P84P (CCT→CCG) | gspK ← | type II secretion system minor pseudopilin GspK |
| RA | NZ_CP022686 | 1,860,077 | G→T | 15.8% | G116G (GGC→GGA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,925,332 | A→C | 12.6% | N151T (AAC→ACC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 2,049,089 | T→G | 16.7% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,094 | G→T | 16.6% | T254T (ACC→ACA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,123,241 | A→C | 17.5% | F208V (TTT→GTT) | tldD ← | metalloprotease TldD |
| RA | NZ_CP022686 | 2,130,829 | A→C | 10.4% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,185,075 | A→C | 14.0% | V46G (GTT→GGT) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,209,074 | C→A | 8.0% | A258A (GCG→GCT) | chiA ← | bifunctional chitinase/lysozyme |
| 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 | 2,357,291 | A→C | 12.3% | N26T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,394,287 | T→G | 20.8% | 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 |
| RA | NZ_CP022686 | 2,572,721 | A→C | 17.3% | F186C (TTT→TGT) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,429 | T→G | 18.0% | 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 | 2,758,168 | A→C | 8.1% | N54H (AAC→CAC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,769,196 | A→C | 13.6% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,801,864 | T→G | 10.3% | L16F (TTA→TTC) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 22.4% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,856 | T→G | 9.9% | K237N (AAA→AAC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 2,981,612 | A→C | 12.0% | T567P (ACC→CCC) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | NZ_CP022686 | 3,020,229 | T→G | 15.8% | 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 | 3,265,096 | G→T | 11.7% | A73E (GCA→GAA) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,348,345 | G→T | 8.6% | intergenic (‑161/‑39) | CIW80_RS16685 ← / → CIW80_RS26495 | inovirus Gp2 family protein/hypothetical protein |
| RA | NZ_CP022686 | 3,390,614 | G→T | 8.1% | A143A (GCC→GCA) | 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 | 3,528,197 | A→C | 9.6% | N50T (AAC→ACC) | carB → | carbamoyl‑phosphate synthase large subunit |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,713,182 | A→C | 15.0% | E39D (GAA→GAC) | yaeR → | VOC family protein |
| RA | NZ_CP022686 | 3,734,367 | T→G | 21.2% | 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 |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,932,481 | T→G | 14.7% | N171T (AAC→ACC) | lacA ← | galactoside O‑acetyltransferase |
| RA | NZ_CP022686 | 4,032,292 | A→C | 19.8% | E106D (GAA→GAC) | glnK → | P‑II family nitrogen regulator |
| RA | NZ_CP022686 | 4,056,962 | C→A | 15.2% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,079,332 | A→C | 14.0% | W169G (TGG→GGG) | ybbO ← | NADP(+)‑dependent aldehyde reductase |
| RA | NZ_CP022686 | 4,368,341 | T→G | 16.2% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,368,380 | T→G | 13.1% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,297 | T→A | 15.8% | V785D (GTT→GAT) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,324 | C→A | 15.6% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,616,669 | A→G | 6.4% | intergenic (+151/+382) | CIW80_RS23075 → / ← CIW80_RS26560 | hypothetical protein/ATP‑binding protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 8.7% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,839,668 | T→G | 24.2% | V150V (GTA→GTC) | minD ← | septum site‑determining protein MinD |
| MC JC | NZ_CP022686 | 4,844,868 | Δ1,662 bp | 100% | [umuD]–[umuC] | [umuD], [umuC] | |
| 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 | 4,918,846 | C→A | 14.3% | Q387H (CAG→CAT) | adhE ← | bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| RA | NZ_CP022686 | 4,919,037 | T→G | 12.8% | T324P (ACC→CCC) | adhE ← | bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| RA | NZ_CP022686 | 4,947,335 | T→G | 13.3% | V42G (GTT→GGT) | rluB → | 23S rRNA pseudouridine(2605) synthase RluB |
| RA | NZ_CP022686 | 4,951,521 | A→C | 16.9% | T39P (ACC→CCC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,041,191 | G→A | 5.7% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 14.3% | 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 | pMUT1‑hok‑empty | 4,123:1 | +T | 94.3% | 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 | 4,130:1 | +T | 93.6% | intergenic (‑348/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| JC | pMUT1‑hok‑empty | 4,132 | Δ3 bp | 95.0% | intergenic (‑350/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,135 | G→A | 100% | intergenic (‑353/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 316–2618 | 3082–2957 | 340–2767 | 5936 [5781] | [5804] 5956 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMUT1‑hok‑empty | 1263–1317 | 3981–1581 | 265–2719 | 2695 [2532] | [2492] 2568 | putative HTH domain protein–putative rom (RNA I inhibition modulator protein) | putative HTH domain protein,uncharacterized protein,hypothetical protein,putative rom (RNA I inhibition modulator protein) |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 2 (0.020) | 105 (0.820) | 51/250 | NT | 98.1% | coding (320/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1524130 | NA (NA) | intergenic (+8/+232) | CIW80_RS07590/syd | IS3‑like element ISEc52 family transposase/SecY‑interacting protein | |||||
| * | ? | NZ_CP022686 | = 262468 | 2 (0.020) | 113 (0.880) | 50/250 | NT | 98.3% | coding (322/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1761697 | NA (NA) | intergenic (‑72/‑70) | CIW80_RS08710/CIW80_RS08720 | IS3‑like element ISEc52 family transposase/IS3‑like element IS600 family transposase | |||||
| * | ? | NZ_CP022686 | 3899666 = | 183 (1.420) | 9 (0.080) | 9/218 | NT | 5.8% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 135 (1.210) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 2102 (0.480) | 2797 (0.630) | 195/250 | NT | 72.3% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 43 (0.010) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 3029 (0.690) | 2154 (0.610) | 157/200 | NT | 63.7% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 40 (0.010) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||