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 | 37,785 | T→G | 6.6% | K3N (AAA→AAC) | ansP ← | L‑asparagine permease |
| RA | NZ_CP022686 | 349,997 | C→A | 12.1% | A221A (GCC→GCA) | yeaH → | YeaH/YhbH family protein |
| RA | NZ_CP022686 | 360,227 | T→G | 21.2% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 360,290 | T→G | 10.0% | 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 | 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 | 26.2% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 24.8% | 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 | 14.9% | 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 | 829,452 | G→T | 24.0% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 21.3% | intergenic (‑56/+171) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 859,943 | T→G | 12.0% | L602V (TTA→GTA) | yehM → | DUF5682 family protein |
| 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 | 9.3% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,172,451 | G→T | 12.4% | D125Y (GAC→TAC) | yfeD → | putative DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 1,174,272 | A→C | 14.2% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,269,551 | T→G | 9.4% | K1124N (AAA→AAC) | CIW80_RS06320 ← | DUF823 domain‑containing adhesin |
| RA | NZ_CP022686 | 1,360,724 | G→T | 10.3% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,479,631 | G→C | 9.5% | intergenic (‑40/+153) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,535,353 | G→T | 30.9% | M31I (ATG→ATT) | fucI → | L‑fucose isomerase |
| RA | NZ_CP022686 | 1,674,224 | T→G | 21.4% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 14.6% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 10.2% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,833,768 | A→C | 14.4% | M460R (ATG→AGG) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,860,070 | C→A | 20.8% | E119* (GAA→TAA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 2,004,466 | G→T | 6.1% | I428I (ATC→ATA) | cyuP ← | amino acid permease |
| RA | NZ_CP022686 | 2,049,089 | T→G | 14.9% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,110,457 | T→G | 16.0% | K12N (AAA→AAC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,110,465 | T→G | 12.0% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,148,118 | C→G | 14.3% | A127G (GCG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 7.6% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,185,071 | A→C | 10.5% | G47G (GGT→GGG) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,185,075 | A→C | 11.2% | V46G (GTT→GGT) | 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 | 2,226,139 | A→C | 6.8% | D9A (GAC→GCC) | crp → | cAMP‑activated global transcriptional regulator CRP |
| 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 | 14.7% | N26T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,516,873 | A→C | 16.7% | K761N (AAA→AAC) | upaG → | trimeric autotransporter adhesin UpaG |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,634,140 | A→C | 11.5% | V27G (GTC→GGC) | dgoD ← | galactonate dehydratase |
| RA | NZ_CP022686 | 2,643,712 | A→C | 15.0% | L413R (CTG→CGG) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | NZ_CP022686 | 2,906,546 | T→G | 6.6% | K46N (AAA→AAC) | cytR ← | DNA‑binding transcriptional regulator CytR |
| RA | NZ_CP022686 | 2,981,612 | A→C | 9.6% | T567P (ACC→CCC) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | NZ_CP022686 | 3,020,229 | T→G | 22.4% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,136,940 | T→G | 12.8% | 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 | 3,297,328 | T→G | 13.5% | V826G (GTA→GGA) | mgtA → | magnesium‑translocating P‑type ATPase |
| RA | NZ_CP022686 | 3,348,342 | A→T | 10.1% | intergenic (‑158/‑42) | 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 | 12.2% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,215 | A→T | 15.0% | intergenic (‑24/+11) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 20.3% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,528,218 | A→C | 6.8% | D57A (GAC→GCC) | 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 | 3,584,545 | T→A | 6.0% | I60N (ATC→AAC) | ilvN → | acetolactate synthase small subunit |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,770,509 | A→T | 12.4% | intergenic (‑245/+218) | 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 | 3,797,506 | C→G | 12.1% | A138G (GCT→GGT) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,800,981 | A→C | 11.9% | pseudogene (1257/1773 nt) | CIW80_RS19080 → | ShlB/FhaC/HecB family hemolysin secretion/activation protein |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,984,841 | T→G | 12.2% | R67R (CGT→CGG) | queA → | tRNA preQ1(34) S‑adenosylmethionine ribosyltransferase‑isomerase QueA |
| RA | NZ_CP022686 | 4,025,387 | C→A | 11.5% | E435* (GAA→TAA) | ybaE ← | SgrR family transcriptional regulator |
| RA | NZ_CP022686 | 4,331,914 | G→T | 15.6% | L297L (CTC→CTA) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,368,380 | T→G | 15.8% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,334 | A→C | 22.3% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,632,182 | T→G | 14.8% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,764,877 | T→G | 15.2% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| 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 | 4,952,020 | T→G | 10.6% | V205G (GTC→GGC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,029,522 | A→C | 7.4% | intergenic (‑113/+28) | uspF ← / ← ompN | universal stress protein UspF/porin OmpN |
| RA | NZ_CP022686 | 5,043,870 | T→C | 7.7% | D1167D (GAT→GAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,879 | C→T | 6.8% | G1170G (GGC→GGT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 1,375 | Δ1 bp | 5.8% | intergenic (–/+342) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 1,376 | Δ1 bp | 93.3% | intergenic (–/+341) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 93.6% | 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 | 352–2618 | 3068–2957 | 340–2717 | 4297 [4283] | [4123] 4597 | [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 | 262466 = | 0 (0.000) | 148 (1.190) | 61/248 | NT | 100% | 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 | 0 (0.000) | 115 (0.930) | 58/248 | NT | 100% | 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_MW240712 | 1 = | 0 (0.000) | 5033 (1.020) +T |
190/246 | NT | 100% | intergenic (–/+206) | –/JNG15_RS00005 | –/helix‑turn‑helix domain‑containing protein |
| ? | NZ_MW240712 | = 3172 | 0 (0.000) | intergenic (+181/–) | mobA/– | plasmid mobilization protein MobA/– | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 1866 (0.460) | 2736 (0.670) | 192/248 | NT | 67.4% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 782 (0.190) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 2810 (0.690) | 2166 (0.660) | 158/198 | NT | 58.9% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 782 (0.240) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||