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 | 87,520 | G→T | 5.6% | R217S (CGT→AGT) | yddA ← | ABC transporter ATP‑binding protein/permease |
| RA | NZ_CP022686 | 236,274 | Δ1 bp | 24.3% | coding (1288/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 360,227 | T→G | 14.2% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 360,246 | T→G | 12.2% | E28D (GAA→GAC) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 372,574 | A→C | 18.2% | 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 | 512,717 | T→G | 21.0% | intergenic (‑217/+13) | sdiA ← / ← yecC | transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC |
| 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 | 14.6% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 23.5% | 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 | 12.8% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 705,703 | G→T | 9.1% | P35P (CCG→CCT) | CIW80_RS03635 → | hypothetical protein |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 764,997 | T→G | 16.3% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 765,008 | A→T | 13.9% | I37I (ATT→ATA) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,452 | G→T | 17.4% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| 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 | 1,000,401 | A→C | 16.1% | V955G (GTG→GGG) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,005,085 | C→A | 14.8% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,011,390 | T→A | 10.5% | intergenic (‑239/‑34) | glpT ← / → glpA | glycerol‑3‑phosphate transporter/anaerobic glycerol‑3‑phosphate dehydrogenase subunit A |
| RA | NZ_CP022686 | 1,145,570 | C→G | 9.9% | L333F (TTG→TTC) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | NZ_CP022686 | 1,209,908 | T→G | 16.4% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,209,910 | T→G | 11.8% | E395D (GAA→GAC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,249,393 | C→A | 9.3% | intergenic (‑40/+46) | uraA ← / ← upp | uracil permease/uracil phosphoribosyltransferase |
| RA | NZ_CP022686 | 1,278,783 | T→G | 10.2% | D242A (GAC→GCC) | bamB ← | outer membrane protein assembly factor BamB |
| RA | NZ_CP022686 | 1,360,724 | G→T | 12.7% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,370,559 | T→G | 15.3% | K98N (AAA→AAC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,370,565 | A→T | 11.8% | I96I (ATT→ATA) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,371,081 | C→A | 16.6% | P32Q (CCA→CAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,479,607 | A→C | 12.5% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,504,355 | T→A | 7.9% | A264A (GCT→GCA) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,547,000 | G→C | 13.6% | intergenic (+22/‑12) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,558,395 | A→C | 10.7% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,564,296 | A→C | 6.3% | L99F (TTA→TTC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,566,203 | A→C | 11.3% | N735T (AAC→ACC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,632,497 | C→A | 8.0% | P165T (CCG→ACG) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,674,248 | T→G | 13.2% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,047 | G→T | 11.9% | M1M (ATG→ATT) † | metK → | methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,716,167 | A→C | 15.9% | N49T (AAC→ACC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,716,180 | A→C | 14.4% | K53N (AAA→AAC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,828,110 | A→C | 6.5% | R85R (CGT→CGG) | gspK ← | type II secretion system minor pseudopilin GspK |
| RA | NZ_CP022686 | 1,833,762 | A→C | 15.5% | L462R (CTG→CGG) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,954,923 | T→G | 15.3% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,049,089 | T→G | 15.5% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,076,556 | C→G | 7.2% | intergenic (+26/‑207) | ispB → / → sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB |
| RA | NZ_CP022686 | 2,110,457 | T→G | 13.6% | K12N (AAA→AAC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,110,465 | T→G | 11.8% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,110,472 | T→G | 6.8% | K7N (AAA→AAC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 10.6% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,109 | T→G | 12.2% | V124G (GTG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,118 | C→G | 9.6% | A127G (GCG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,163,522 | C→A | 7.6% | 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 | 2,233,674 | C→G | 7.4% | V371V (GTC→GTG) | tsgA → | MFS transporter TsgA |
| 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 | 22.5% | N37T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,361,489 | T→G | 17.8% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,386,496 | T→G | 6.8% | K417N (AAA→AAC) | prlC ← | oligopeptidase A |
| RA | NZ_CP022686 | 2,394,287 | T→G | 15.3% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,398,896 | A→C | 10.1% | 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 | 2,436,695 | A→C | 5.7% | G299G (GGT→GGG) | bcsZ ← | cellulose synthase complex periplasmic endoglucanase BcsZ |
| RA | NZ_CP022686 | 2,460,581 | A→C | 24.3% | intergenic (‑3/‑155) | yhjY ← / → tag | autotransporter outer membrane beta‑barrel domain‑containing protein/DNA‑3‑methyladenine glycosylase I |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,717,400 | T→G | 9.5% | L101V (TTA→GTA) | ilvA → | threonine ammonia‑lyase, biosynthetic |
| RA | NZ_CP022686 | 2,736,578 | C→A | 8.9% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,601 | G→T | 11.9% | intergenic (+16/‑27) | CIW80_RS13750 → / → CIW80_RS13755 | tRNA‑Leu/tRNA‑Pro |
| RA | NZ_CP022686 | 2,758,109 | A→C | 8.6% | N34T (AAC→ACC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,769,166 | C→A | 10.1% | C57F (TGC→TTC) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,780,110 | T→G | 9.9% | F677C (TTT→TGT) | metE → | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
| RA | NZ_CP022686 | 2,834,886 | A→C | 10.5% | K597N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 25.0% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 10.9% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,915 | T→G | 9.8% | T218P (ACC→CCC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 2,920,418 | C→A | 9.4% | A65E (GCA→GAA) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 3,020,229 | T→G | 11.7% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,090,101 | A→C | 9.5% | V9G (GTT→GGT) | yjcB ← | YjcB family protein |
| RA | NZ_CP022686 | 3,114,640 | A→C | 5.9% | G40G (GGT→GGG) | CIW80_RS15500 ← | ABC transporter ATP‑binding protein |
| RA | NZ_CP022686 | 3,136,940 | T→G | 13.2% | 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 | 3,265,084 | T→G | 21.3% | N77T (AAC→ACC) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,281,030 | C→A | 15.5% | F83L (TTC→TTA) | yjfF → | sugar ABC transporter permease YjfF |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,504,054 | T→G | 9.7% | V204G (GTT→GGT) | tal → | transaldolase |
| RA | NZ_CP022686 | 3,570,234 | T→G | 7.3% | L217V (TTG→GTG) | yabI → | DedA family protein |
| RA | NZ_CP022686 | 3,652,115 | A→T | 8.6% | V418V (GTT→GTA) | CIW80_RS18255 ← | 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 | 23.5% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,770,509 | A→T | 9.7% | 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 | 3,797,481 | T→G | 15.5% | L130V (TTA→GTA) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,798,081 | A→T | 7.4% | I330F (ATC→TTC) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,824,324 | A→C | 12.5% | S215R (AGC→CGC) | CIW80_RS19155 → | TolC family protein |
| RA | NZ_CP022686 | 3,852,459 | T→G | 10.4% | N178T (AAC→ACC) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,868,846 | T→G | 14.6% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,928,356 | T→G | 9.3% | A280A (GCT→GCG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 15.9% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 8.4% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,004,135 | T→G | 9.4% | R29R (CGT→CGG) | yajQ → | nucleotide binding protein YajQ |
| RA | NZ_CP022686 | 4,014,241 | G→T | 13.3% | intergenic (+87/‑257) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,196,276 | T→G | 12.8% | E15D (GAA→GAC) | holA ← | DNA polymerase III subunit delta |
| RA | NZ_CP022686 | 4,280,095 | T→G | 8.8% | G103G (GGT→GGG) | cydB → | cytochrome d ubiquinol oxidase subunit II |
| RA | NZ_CP022686 | 4,290,635 | T→G | 6.1% | T109P (ACC→CCC) | ybgS ← | YbgS‑like family protein |
| RA | NZ_CP022686 | 4,368,380 | T→G | 12.4% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,620,262 | A→C | 10.3% | intergenic (+6/+117) | CIW80_RS23110 → / ← CIW80_RS26565 | Exc2 family lipoprotein/hypothetical protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 9.5% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,951 | A→C | 11.3% | N732T (AAC→ACC) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,678,047 | A→C | 28.4% | intergenic (+45/‑76) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,712,764 | G→C | 11.7% | A52G (GCT→GGT) | yceB ← | lipoprotein |
| RA | NZ_CP022686 | 4,809,441 | T→G | 10.0% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,839,687 | T→G | 10.2% | N144T (AAC→ACC) | minD ← | septum site‑determining protein MinD |
| 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 | 4,905,174 | C→G | 13.4% | G100G (GGC→GGG) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 4,980,886 | A→T | 9.8% | P104P (CCT→CCA) | sapD ← | peptide ABC transporter ATP‑binding protein SapD |
| RA | NZ_CP022686 | 5,041,191 | G→A | 5.2% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 12.9% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,182 | T→A | 8.1% | G1271G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 93.2% | 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 | 189–2618 | 3085–2957 | 340–2897 | 10616 [9780] | [10444] 10606 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMUT1‑hok‑empty | 1262–1369 | 3983–1582 | 214–2722 | 4296 [4291] | [4238] 4322 | 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 | 3899666 = | 85 (0.490) | 109 (0.720) | 49/216 | NT | 60.9% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 66 (0.440) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 80 (0.460) | 118 (0.780) | 55/216 | NT | 63.5% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 66 (0.440) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 3311 (0.450) | 4533 (0.620) | 215/248 | NT | 66.3% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 1292 (0.180) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 4953 (0.670) | 3731 (0.630) | 174/198 | NT | 58.7% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 1289 (0.220) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||