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 | 311,453 | G→T | 9.9% | D116Y (GAT→TAT) | ydjY → | lipoprotein YdjY |
| RA | NZ_CP022686 | 360,227 | T→G | 15.4% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 372,574 | A→C | 19.6% | 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 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 651,848 | A→C | 11.3% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 693,021 | A→C | 10.0% | T121P (ACG→CCG) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 694,391 | C→A | 10.1% | intergenic (+151/‑45) | 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 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,435 | C→A | 23.3% | intergenic (‑24/+203) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,441 | C→A | 22.7% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 17.7% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| 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 | 957,112 | T→G | 12.8% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,005,085 | C→A | 10.8% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,047,906 | G→T | 9.3% | intergenic (‑136/+28) | nuoM ← / ← nuoL | NADH‑quinone oxidoreductase subunit M/NADH‑quinone oxidoreductase subunit L |
| RA | NZ_CP022686 | 1,174,272 | A→C | 11.6% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 18.9% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,280,117 | T→G | 6.4% | N8H (AAC→CAC) | yfgM ← | ancillary SecYEG translocon subunit YfgM |
| RA | NZ_CP022686 | 1,360,724 | G→T | 16.4% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,729 | G→T | 12.6% | intergenic (‑64/+260) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,370,556 | T→G | 21.4% | P99P (CCA→CCC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,370,559 | T→G | 13.3% | K98N (AAA→AAC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,371,086 | G→T | 20.2% | E34* (GAA→TAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,424,362 | A→T | 10.9% | intergenic (‑58/+5) | CIW80_RS07085 ← / ← CIW80_RS07090 | tRNA‑Arg/tRNA‑Arg |
| RA | NZ_CP022686 | 1,452,244 | A→C | 7.0% | G419G (GGT→GGG) | hycC ← | formate hydrogenlyase subunit 3 |
| RA | NZ_CP022686 | 1,504,280 | C→G | 8.4% | C239W (TGC→TGG) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,558,395 | A→C | 10.3% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,566,217 | A→C | 17.9% | T740P (ACG→CCG) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 9.7% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,640,925 | A→C | 15.7% | R7S (AGA→AGC) | ygfM → | molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,224 | T→G | 16.4% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 12.1% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,705,997 | C→A | 14.9% | intergenic (‑607/‑48) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,716,167 | A→C | 9.5% | N49T (AAC→ACC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,716,202 | A→C | 9.4% | T61P (ACC→CCC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,805,047 | G→T | 16.1% | pseudogene (328/934 nt) | CIW80_RS09020 → | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
| RA | NZ_CP022686 | 1,860,060 | T→G | 16.4% | K122T (AAA→ACA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,860,077 | G→T | 14.8% | G116G (GGC→GGA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,865,103 | A→C | 7.1% | L491V (TTG→GTG) | pitB ← | inorganic phosphate transporter PitB |
| RA | NZ_CP022686 | 1,925,365 | A→C | 9.0% | D162A (GAC→GCC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,965,173 | A→C | 9.8% | R86R (CGT→CGG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 2,035,513 | T→A | 5.8% | Y141F (TAT→TTT) | rsmI ← | 16S rRNA (cytidine(1402)‑2'‑O)‑methyltransferase |
| RA | NZ_CP022686 | 2,046,901 | A→C | 5.2% | G304G (GGT→GGG) | mtr ← | tryptophan permease |
| RA | NZ_CP022686 | 2,049,089 | T→G | 16.1% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,112 | C→A | 10.0% | A248A (GCG→GCT) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,076,554 | T→G | 10.2% | intergenic (+24/‑209) | ispB → / → sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB |
| RA | NZ_CP022686 | 2,148,122 | T→G | 15.1% | S128R (AGT→AGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,145 | T→G | 10.6% | V136G (GTT→GGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,160 | T→G | 13.6% | V141G (GTG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,272,831 | G→T | 5.7% | intergenic (+73/‑24) | greB → / → yhgF | transcription elongation factor GreB/Tex family protein |
| RA | NZ_CP022686 | 2,305,971 | G→T | 11.4% | S222* (TCA→TAA) | CIW80_RS11625 ← | fimbrial biogenesis usher protein |
| RA | NZ_CP022686 | 2,310,429 | T→G | 9.0% | N248T (AAC→ACC) | glgP ← | glycogen phosphorylase |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,380,936 | A→C | 9.3% | K186N (AAA→AAC) | pitA → | inorganic phosphate transporter PitA |
| RA | NZ_CP022686 | 2,380,955 | A→C | 7.5% | T193P (ACC→CCC) | pitA → | inorganic phosphate transporter PitA |
| RA | NZ_CP022686 | 2,386,496 | T→G | 8.7% | K417N (AAA→AAC) | prlC ← | oligopeptidase A |
| RA | NZ_CP022686 | 2,397,370 | T→G | 12.4% | F9C (TTT→TGT) | chuT → | heme ABC transporter substrate‑binding protein ChuT |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,517,086 | A→C | 5.8% | K832N (AAA→AAC) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,546,394 | A→C | 24.0% | V95G (GTT→GGT) | waaG ← | glycosyltransferase family 4 protein |
| RA | NZ_CP022686 | 2,546,423 | A→C | 21.7% | 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 | 2,617,829 | T→G | 6.1% | N209T (AAC→ACC) | ilvB ← | acetolactate synthase large subunit |
| RA | NZ_CP022686 | 2,717,400 | T→G | 9.6% | L101V (TTA→GTA) | ilvA → | threonine ammonia‑lyase, biosynthetic |
| RA | NZ_CP022686 | 2,733,571 | T→G | 8.8% | F53V (TTT→GTT) | rffG → | dTDP‑glucose 4,6‑dehydratase |
| RA | NZ_CP022686 | 2,743,601 | G→T | 14.5% | intergenic (+16/‑27) | CIW80_RS13750 → / → CIW80_RS13755 | tRNA‑Leu/tRNA‑Pro |
| RA | NZ_CP022686 | 2,801,817 | T→G | 9.6% | Y32S (TAC→TCC) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 22.8% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 11.8% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,874,073 | A→C | 10.6% | T62P (ACC→CCC) | CIW80_RS14390 → | carbohydrate porin |
| RA | NZ_CP022686 | 3,020,229 | T→G | 11.1% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,086,803 | A→C | 7.7% | V718G (GTA→GGA) | uvrA ← | excinuclease ABC subunit UvrA |
| RA | NZ_CP022686 | 3,136,935 | T→G | 11.1% | S163R (AGC→CGC) | 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 | 3,239,387 | T→G | 7.2% | V396G (GTC→GGC) | ulaA → | PTS ascorbate transporter subunit IIC |
| RA | NZ_CP022686 | 3,297,328 | T→G | 13.0% | V826G (GTA→GGA) | mgtA → | magnesium‑translocating P‑type ATPase |
| RA | NZ_CP022686 | 3,297,360 | T→G | 10.7% | L837V (TTA→GTA) | mgtA → | magnesium‑translocating P‑type ATPase |
| RA | NZ_CP022686 | 3,387,616 | G→T | 9.1% | I231I (ATC→ATA) | sgcQ ← | BtpA family protein SgcQ |
| 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 | 14.2% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,214 | T→A | 11.5% | intergenic (‑23/+12) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,215 | A→T | 14.0% | intergenic (‑24/+11) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 20.4% | 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 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,703,648 | A→C | 8.4% | T120P (ACG→CCG) | fabZ → | 3‑hydroxyacyl‑ACP dehydratase FabZ |
| RA | NZ_CP022686 | 3,734,367 | T→G | 18.0% | 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 | 3,868,925 | A→C | 9.5% | R356R (CGT→CGG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,925,289 | A→C | 16.1% | N156T (AAC→ACC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 10.3% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 13.3% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,056,957 | A→T | 9.5% | K136* (AAA→TAA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,079,332 | A→C | 11.7% | W169G (TGG→GGG) | ybbO ← | NADP(+)‑dependent aldehyde reductase |
| RA | NZ_CP022686 | 4,331,940 | A→C | 19.0% | F289V (TTT→GTT) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,412,284 | A→C | 16.5% | W241G (TGG→GGG) | ybjT ← | SDR family oxidoreductase |
| RA | NZ_CP022686 | 4,440,324 | C→A | 15.2% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,334 | A→G | 16.2% | Q797Q (CAA→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,535,285 | A→C | 9.9% | K97T (AAG→ACG) | appA → | bifunctional acid phosphatase/4‑phytase |
| RA | NZ_CP022686 | 4,667,824 | A→C | 5.5% | T327P (ACC→CCC) | CIW80_RS23390 → | GTP‑binding protein |
| RA | NZ_CP022686 | 4,764,877 | T→G | 14.5% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,896 | C→G | 10.3% | intergenic (‑76/‑185) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,783,334 | A→C | 21.4% | V32G (GTC→GGC) | mnmA ← | tRNA 2‑thiouridine(34) synthase MnmA |
| RA | NZ_CP022686 | 4,809,441 | T→G | 12.3% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,812,919 | A→C | 6.7% | D233A (GAC→GCC) | CIW80_RS24290 → | phage tail tape measure protein |
| 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 | 4,905,159 | C→A | 21.5% | F95L (TTC→TTA) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 4,916,128 | A→C | 8.5% | intergenic (+255/+30) | tdk → / ← CIW80_RS24885 | thymidine kinase/IS4 family transposase |
| RA | NZ_CP022686 | 4,980,886 | A→C | 12.0% | P104P (CCT→CCG) | sapD ← | peptide ABC transporter ATP‑binding protein SapD |
| RA | NZ_CP022686 | 5,042,304 | T→C | 10.4% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,385 | T→C | 6.6% | G672G (GGT→GGC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,347 | A→G | 6.0% | N993S (AAT→AGT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,870 | T→C | 7.0% | D1167D (GAT→GAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,149 | T→A | 12.3% | G1260G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,356 | T→C | 5.8% | V1329V (GTT→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| JC | pHH‑29_RBS | 1,780 | Δ11 bp | 91.8% | coding (282‑292/570 nt) | Aldafermin (NGM282) → | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 692–2619 | 3034–2957 | 339–2343 | 4769 [4524] | [4516] 4747 | JNG15_RS00010–mobA | JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2769–2907 | 5512–3105 | 199–2744 | 6229 [5882] | [5353] 6243 | 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 | 262466 = | 2 (0.010) | 138 (0.830) | 72/248 | NT | 98.6% | 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 (0.010) | 156 (0.940) | 65/248 | NT | 98.7% | 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 | |||||