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 | position | mutation | freq | annotation | gene | description |
| RA | 119,120 | T→C | 33.3% | V181A (GTC→GCC) | pdhR → | pyruvate dehydrogenase complex repressor; autorepressor |
| RA | 161,068 | A→C | 27.5% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 234,994 | G→T | 14.4% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,010 | G→T | 16.2% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,019 | C→A | 19.1% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,022 | G→T | 27.7% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 295,695 | T→G | 19.0% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 297,724 | A→C | 10.9% | D187E (GAT→GAG) | paoA ← | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| RA | 345,428 | T→C | 11.6% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 353,486 | A→T | 6.5% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 353,489 | C→T | 6.2% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 360,157 | T→G | 8.2% | intergenic (‑91/+504) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,165 | G→C | 6.1% | intergenic (‑99/+496) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,173 | C→A | 7.0% | intergenic (‑107/+488) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,181 | G→C | 6.8% | intergenic (‑115/+480) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,752 | A→G | 100% | V331A (GTG→GCG) | lacI ← | DNA‑binding transcriptional repressor |
| JC | 361,139 | +GCCA | 9.5% | coding (605/1083 nt) | lacI ← | DNA‑binding transcriptional repressor |
| RA | 361,806 | G→A | 100% | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor/mhp operon transcriptional activator |
| RA | 370,428 | T→C | 6.3% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 560,192 | A→C | 5.7% | noncoding (14/77 nt) | argU → | tRNA‑Arg |
| RA | 667,017 | T→G | 11.8% | E15D (GAA→GAC) | holA ← | DNA polymerase III, delta subunit |
| RA | 877,980 | G→T | 6.1% | Q71K (CAA→AAA) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
| RA | 919,147:1 | +T | 8.0% | coding (428/2277 nt) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,282,421 | A→T | 12.1% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,334,735 | A→C | 13.0% | K79T (AAG→ACG) | yciS → | DUF1049 family inner membrane protein, function unknown |
| RA | 1,345,484 | A→C | 8.5% | intergenic (‑188/+180) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| JC JC | 1,376,043 | IS5 (–) +4 bp | 40.3% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,628,207 | G→A | 24.8% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
| RA | 1,632,204 | C→A | 31.5% | intergenic (‑165/+7) | gnsB ← / ← ynfN | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)/Qin prophage; cold shock‑induced protein |
| RA | 1,673,381 | C→A | 6.4% | S233* (TCA→TAA) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,701,282 | A→C | 7.7% | Q36P (CAG→CCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,966 | T→A | 5.2% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,975 | G→A | 7.7% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,071 | A→T | 7.7% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,796,428 | C→A | 51.7% | V134F (GTC→TTC) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,823,835 | A→C | 7.6% | W53G (TGG→GGG) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 1,823,843 | A→C | 9.1% | F50C (TTT→TGT) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 2,109,270 | G→T | 7.5% | N36K (AAC→AAA) | wcaM ← | colanic acid biosynthesis protein |
| RA | 2,170,713 | C→A | 24.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,724 | G→T | 19.9% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,298,128 | C→T | 9.5% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,159 | T→C | 7.9% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,492 | A→G | 7.5% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,423,366 | C→A | 10.0% | E118* (GAA→TAA) | purF ← | amidophosphoribosyltransferase |
| RA | 2,463,915 | C→A | 28.4% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,547,821 | A→C | 6.8% | L241V (TTG→GTG) | eutR ← | eut operon transcriptional activator, AraC family |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,834,267 | A→T | 5.4% | E462V (GAG→GTG) | ascF → | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
| RA | 2,908,686 | G→T | 11.8% | E91* (GAA→TAA) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 3,039,409 | T→G | 19.5% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,049,716 | A→T | 6.4% | V39V (GTA→GTT) | fau → | 5‑formyltetrahydrofolate cyclo‑ligase family protein |
| RA | 3,080,755 | T→G | 20.5% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,385,662 | C→G | 8.1% | intergenic (‑275/+155) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,392,594 | A→C | 5.9% | A248A (GCT→GCG) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,416,666 | T→G | 11.3% | intergenic (+113/+116) | yhdZ → / ← rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| RA | 3,439,422 | G→T | 8.0% | I26I (ATC→ATA) | rplF ← | 50S ribosomal subunit protein L6 |
| RA | 3,469,859 | G→T | 10.0% | intergenic (‑60/+107) | yheO ← / ← fkpA | putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 3,519,657 | G→T | 100% | intergenic (‑149/‑171) | nudE ← / → yrfF | adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein |
| JC | 3,553,834 | Δ54 bp | 5.6% | coding (79‑132/759 nt) | glpR ← | GlpR DNA‑binding transcriptional repressor |
| RA | 3,721,469 | A→C | 8.5% | D421E (GAT→GAG) | xylB ← | xylulokinase |
| RA | 3,721,480 | T→G | 8.1% | T418P (ACG→CCG) | xylB ← | xylulokinase |
| RA | 3,774,382 | T→G | 11.9% | intergenic (+5/‑193) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,779,281 | C→G | 7.0% | A221G (GCT→GGT) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,803,467 | G→A | 6.7% | D95N (GAT→AAT) | coaD → | pantetheine‑phosphate adenylyltransferase |
| RA | 3,816,601 | A→T | 36.2% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,822,339 | A→C | 15.5% | Q12P (CAA→CCA) ‡ | xanP → | xanthine permease |
| RA | 3,822,340 | A→C | 14.4% | Q12H (CAA→CAC) ‡ | xanP → | xanthine permease |
| RA | 3,822,345 | T→G | 9.3% | V14G (GTT→GGT) | xanP → | xanthine permease |
| RA | 3,872,511 | A→C | 5.3% | V323V (GTT→GTG) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,960,036 | G→A | 15.9% | R87H (CGC→CAC) | rho → | transcription termination factor |
| RA | 4,027,520 | G→T | 7.9% | C339F (TGT→TTT) | trkH → | potassium transporter |
| RA | 4,076,055 | T→G | 9.2% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,085,145 | A→C | 8.3% | A194A (GCT→GCG) | frvB ← | putative PTS enzyme, IIB component/IIC component |
| RA | 4,285,857 | T→C | 7.5% | intergenic (+135/+396) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,285,892 | A→G | 6.6% | intergenic (+170/+361) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,083 | T→C | 12.9% | intergenic (+361/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,118 | A→G | 5.3% | intergenic (+396/+135) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,297,846 | C→A | 14.1% | M150I (ATG→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,554,122 | A→C | 5.4% | F129V (TTC→GTC) | yjiL ← | putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehydratase |
| RA | 4,603,125 | A→C | 7.6% | T300P (ACG→CCG) | yjjU → | putative patatin‑like family phospholipase |
| RA | 4,604,195 | A→G | 6.7% | intergenic (+118/+302) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 373903 | 375054 | 1152 | 91 [85] | [87] 89 | frmA | frmA |
| * | * | ÷ | CP009273 | 4100668 | 4101490 | 823 | 90 [87] | [87] 91 | [tpiA] | [tpiA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 268 (0.920) | 227 (0.780) | 124/278 | NT | 45.9% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 360278 | NA (NA) | 9911 (36.120) +TTAATTAA |
195/262 | NT | 96.7% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 361823 | 363 (1.250) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
| * | ? | CP009273 | 360652 = | 409 (1.400) | 9090 (46.810) +46 bp |
186/186 | NT | 97.6% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 1317577 | 269 (0.920) | coding (101/882 nt) | yciV | PHP domain protein | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 36 (0.120) | 26/278 | NT | 26.9% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 566411 = | 98 (0.340) | coding (63/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | = 378046 | NA (NA) | 34 (0.120) | 19/278 | NT | 26.6% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 566415 | 94 (0.320) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | 776825 = | 205 (0.700) | 28 (0.100) +G |
12/276 | NT | 12.2% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | CP009273 | = 2514488 | 202 (0.690) | noncoding (216/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 776902 | 169 (0.580) | 12 (0.050) | 8/238 | NT | 7.9% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777267 = | 134 (0.540) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | 1203246 = | 161 (0.550) | 77 (0.300) | 47/246 | NT | 36.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 124 (0.480) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 160 (0.550) | 134 (0.520) | 76/246 | NT | 50.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 124 (0.480) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2007609 | 254 (0.870) | 29 (0.100) | 23/266 | NT | 10.7% | coding (900/1659 nt) | fliF | flagellar basal‑body MS‑ring and collar protein |
| ? | CP009273 | 2021385 = | 239 (0.860) | coding (114/1695 nt) | yedQ | putative membrane‑anchored diguanylate cyclase | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 34 (0.120) | 28/278 | NT | 10.3% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | = 3904781 | 295 (1.010) | coding (105/1041 nt) | pstS | periplasmic phosphate binding protein, high‑affinity | |||||
| * | ? | CP009273 | 3904777 = | 301 (1.030) | 28 (0.100) | 19/278 | NT | 8.5% | coding (109/1041 nt) | pstS | periplasmic phosphate binding protein, high‑affinity |
| ? | CP009273 | 4487998 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | CP009273 | 4532499 = | 50 (0.170) | 39 (0.140) | 29/260 | NT | 38.5% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 78 (0.290) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 50 (0.170) | 52 (0.190) | 40/260 | NT | 45.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 78 (0.290) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||