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 | 238,324 | G→C | 17.7% | V85V (GTC→GTG) | sufE ← | cysteine desulfuration protein SufE |
| RA | NZ_CP022686 | 298,027 | A→C | 9.6% | F60C (TTT→TGT) | chbC ← | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
| RA | NZ_CP022686 | 372,574 | A→C | 15.8% | 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 | 22.2% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 15.7% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| 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 | 17.0% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 13.9% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 864,173 | T→G | 24.5% | intergenic (+39/+2) | yehR → / ← yehS | YehR family lipoprotein/DUF1456 family protein |
| RA | NZ_CP022686 | 881,739 | A→C | 28.8% | intergenic (+254/+133) | 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 | 1,237,910 | A→C | 18.2% | F306V (TTT→GTT) | tmcA ← | tRNA cytosine(34) acetyltransferase TmcA |
| RA | NZ_CP022686 | 1,280,117 | T→G | 12.3% | N8H (AAC→CAC) | yfgM ← | ancillary SecYEG translocon subunit YfgM |
| RA | NZ_CP022686 | 1,370,559 | T→G | 16.7% | K98N (AAA→AAC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,371,081 | C→A | 20.5% | P32Q (CCA→CAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,482,223 | T→A | 94.4% | M293L (ATG→TTG) | cysD ← | sulfate adenylyltransferase subunit CysD |
| RA | NZ_CP022686 | 1,564,543 | A→C | 8.9% | S182R (AGC→CGC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,674,244 | T→G | 16.8% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 15.7% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,833,745 | T→G | 17.0% | N468H (AAC→CAC) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,881,530 | A→C | 9.3% | V149G (GTC→GGC) | exbB ← | tol‑pal system‑associated acyl‑CoA thioesterase |
| RA | NZ_CP022686 | 2,049,097 | A→T | 16.1% | R253R (CGT→CGA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,076,554 | T→G | 10.4% | intergenic (+24/‑209) | ispB → / → sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB |
| RA | NZ_CP022686 | 2,163,522 | C→A | 6.2% | intergenic (‑17/+23) | rrf ← / ← CIW80_RS10805 | 5S ribosomal RNA/tRNA‑Thr |
| 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 | 2,361,489 | T→G | 12.1% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,386,496 | T→G | 11.3% | K417N (AAA→AAC) | prlC ← | oligopeptidase A |
| RA | NZ_CP022686 | 2,394,287 | T→G | 17.7% | 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 | 2,460,514 | G→C | 11.5% | A22G (GCC→GGC) | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,572,705 | A→C | 12.9% | G191G (GGT→GGG) | CIW80_RS12885 ← | ROK family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,719,161 | A→T | 7.8% | L124H (CTC→CAC) | ilvY ← | HTH‑type transcriptional activator IlvY |
| RA | NZ_CP022686 | 2,769,181 | A→C | 14.2% | V52G (GTG→GGG) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,769,196 | A→C | 19.6% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,868,740 | T→G | 18.1% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 10.6% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,913,769 | A→C | 9.1% | H611P (CAC→CCC) | metL → | bifunctional aspartate kinase/homoserine dehydrogenase II |
| RA | NZ_CP022686 | 2,920,411 | G→T | 10.9% | E63* (GAA→TAA) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 2,920,418 | C→A | 6.8% | A65E (GCA→GAA) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 2,920,428 | A→C | 9.0% | K68N (AAA→AAC) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 2,937,239 | T→G | 7.2% | T209P (ACG→CCG) | yijO ← | AraC family transcriptional regulator |
| RA | NZ_CP022686 | 3,136,940 | T→G | 14.2% | D161A (GAC→GCC) | phnN ← | ribose 1,5‑bisphosphokinase |
| RA | NZ_CP022686 | 3,163,945 | A→C | 8.1% | T397P (ACG→CCG) | melA → | alpha‑galactosidase |
| RA | NZ_CP022686 | 3,163,954 | A→C | 7.4% | T400P (ACC→CCC) | 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 | 3,200,595 | A→C | 9.7% | V199G (GTT→GGT) | frdA ← | fumarate reductase (quinol) flavoprotein subunit |
| 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 | 16.7% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,229 | T→G | 17.8% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,652,083 | C→G | 9.1% | intergenic (‑92/+20) | panB ← / ← CIW80_RS18255 | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin |
| 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 | 17.9% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,748,050 | T→G | 8.2% | K22N (AAA→AAC) | CIW80_RS18735 ← | hypothetical 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 | 3,935,324 | T→G | 15.9% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 4,194,942 | T→G | 10.6% | T116P (ACC→CCC) | nadD ← | nicotinate‑nucleotide adenylyltransferase |
| RA | NZ_CP022686 | 4,461,732 | T→G | 9.4% | intergenic (+86/‑84) | aroA → / → ycaL | 3‑phosphoshikimate 1‑carboxyvinyltransferase/metallopeptidase YcaL |
| 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 | pMUT1‑hok‑empty | 4,123:1 | +T | 94.2% | 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 | 342–2618 | 3068–2957 | 340–2727 | 3824 [3724] | [3425] 3815 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMUT1‑hok‑empty | 1257–1395 | 3985–1723 | 329–2729 | 2019 [2008] | [2016] 2023 | 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 = | 0 (0.000) | 108 (0.900) | 58/248 | 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) | 101 (0.850) | 55/248 | 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 | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 1496 (0.440) | 2144 (0.640) | 183/248 | NT | 67.1% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 602 (0.180) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 2124 (0.630) | 1743 (0.650) | 149/198 | NT | 60.3% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 605 (0.230) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||