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 | 169,092 | T→G | 8.3% | L382V (TTG→GTG) | fhuB → | fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components |
| RA | 189,874 | A→C | 12.7% | E172D (GAA→GAC) | frr → | ribosome recycling factor |
| RA | 234,984 | G→T | 16.5% | I80I (ATC→ATA) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 234,985 | A→T | 13.4% | I80N (ATC→AAC) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 234,990 | G→T | 21.3% | F78L (TTC→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 234,994 | G→T | 25.4% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,006 | G→T | 15.5% | T73K (ACG→AAG) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,010 | G→T | 23.7% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,019 | C→A | 32.6% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,022 | G→T | 27.3% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,036 | G→T | 20.7% | S63Y (TCC→TAC) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 260,917 | T→G | 5.5% | M1M (ATG→CTG) † | yafX ← | CP4‑6 prophage; uncharacterized protein |
| RA | 295,695 | T→G | 17.0% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 345,428 | T→C | 9.3% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 353,486 | A→T | 7.6% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 353,489 | C→T | 7.2% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 360,752 | A→G | 100% | V331A (GTG→GCG) | lacI ← | DNA‑binding transcriptional repressor |
| JC | 361,139 | +GCCA | 17.7% | 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 | 418,995 | T→G | 10.5% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 450,333 | A→T | 9.4% | intergenic (+88/‑256) | bolA → / → tig | stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor) |
| JC JC | 919,057 | IS5 (–) +4 bp | 66.6% | coding (338‑341/2277 nt) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 960,265 | T→G | 10.4% | F164V (TTT→GTT) | ycaI → | ComEC family inner membrane protein |
| RA | 1,088,617 | C→A | 5.1% | Q96K (CAG→AAG) | ycdT → | diguanylate cyclase, membrane‑anchored |
| RA | 1,118,506 | A→T | 8.2% | L75Q (CTA→CAA) | yceB ← | lipoprotein, DUF1439 family |
| RA | 1,118,542 | C→G | 8.0% | S63T (AGC→ACC) | yceB ← | lipoprotein, DUF1439 family |
| RA | 1,207,958 | G→T | 11.4% | intergenic (‑499/+201) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| JC JC | 1,376,043 | IS5 (–) +4 bp | 27.5% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,460,593 | C→G | 5.5% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,498,612 | C→A | 11.2% | R213R (CGC→CGA) | insQ → | IS609 transposase B |
| RA | 1,588,311 | T→G | 6.1% | pseudogene (3934/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,628,207 | G→A | 19.1% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
| RA | 1,630,704 | C→G | 15.2% | intergenic (‑80/‑309) | nohQ ← / → ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| RA | 1,662,682 | A→G | 5.5% | I47T (ATC→ACC) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| RA | 1,703,071 | A→T | 6.4% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,101 | C→G | 6.5% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,795,380 | A→T | 68.4% | V483E (GTA→GAA) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,796,428 | C→A | 6.0% | 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 | 7.3% | F50C (TTT→TGT) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 1,859,011 | C→G | 7.2% | intergenic (+20/+28) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 2,011,734 | Δ1 bp | 100% | coding (308/444 nt) | fliJ → | flagellar protein |
| RA | 2,080,674 | G→T | 8.1% | intergenic (‑79/+136) | yoeI ← / ← yeeY | uncharacterized protein/LysR family putative transcriptional regulator |
| RA | 2,170,708 | G→T | 10.2% | intergenic (‑25/+283) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,713 | C→A | 28.6% | 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 | 28.2% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,757 | T→A | 9.2% | intergenic (‑74/+234) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,298,128 | C→T | 9.4% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,303,607 | A→C | 10.3% | L93R (CTG→CGG) | ada ← | fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase |
| RA | 2,463,906 | C→A | 19.6% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,910 | G→T | 18.8% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,915 | C→A | 14.2% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,587,434 | T→A | 5.7% | L595F (TTA→TTT) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
| JC | 2,713,645 | +CCTGCGC | 71.3% | coding (334/2661 nt) | pka → | protein lysine acetyltransferase |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| JC | 2,811,717 | Δ134 bp | 7.9% | [argV] | [argV] | |
| RA | 2,835,291 | T→G | 10.9% | C315G (TGC→GGC) | ascB → | cryptic 6‑phospho‑beta‑glucosidase |
| RA | 2,940,829 | A→T | 7.4% | intergenic (+7/‑27) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,039,409 | T→G | 17.7% | 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 | 3,080,755 | T→G | 13.9% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,080,759 | T→G | 6.1% | V232G (GTT→GGT) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,263,502 | C→T | 5.2% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,385,479 | C→G | 8.4% | intergenic (‑92/+338) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,385,518 | G→C | 6.4% | intergenic (‑131/+299) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,416,890 | T→G | 6.0% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| 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 |
| RA | 3,525,215 | A→C | 13.9% | L195R (CTG→CGG) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,525,232 | T→A | 12.0% | L189F (TTA→TTT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,546,277 | A→T | 9.6% | intergenic (‑445/‑167) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,774,382 | T→G | 6.2% | 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 | 8.4% | A221G (GCT→GGT) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,779,316 | G→T | 6.1% | D233Y (GAT→TAT) ‡ | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,779,317 | A→T | 7.3% | D233V (GAT→GTT) ‡ | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,786,687 | C→A | 8.2% | L119F (TTG→TTT) | yibB ← | YibB family protein, function unknown |
| RA | 3,816,601 | A→T | 25.7% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,822,339 | A→C | 7.2% | Q12P (CAA→CCA) ‡ | xanP → | xanthine permease |
| RA | 3,822,340 | A→C | 15.4% | Q12H (CAA→CAC) ‡ | xanP → | xanthine permease |
| RA | 3,822,346 | T→G | 8.5% | V14V (GTT→GTG) | xanP → | xanthine permease |
| RA | 3,870,977 | T→A | 5.4% | intergenic (‑152/+88) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
| RA | 3,871,017 | A→T | 6.9% | intergenic (‑192/+48) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
| RA | 3,948,383 | T→G | 5.9% | F516V (TTC→GTC) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,952,817 | T→G | 8.9% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,960,036 | G→A | 9.1% | R87H (CGC→CAC) | rho → | transcription termination factor |
| RA | 4,076,055 | T→G | 15.9% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,080,364 | G→T | 7.7% | M1M (ATG→ATT) † | yiiG → | DUF3829 family lipoprotein |
| RA | 4,297,846 | C→A | 9.7% | M150I (ATG→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,468,993 | A→T | 6.0% | F121Y (TTC→TAC) | yjgM ← | putative acetyltransferase |
| RA | 4,575,840 | A→C | 9.1% | pseudogene (793/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| RA | 4,603,125 | A→C | 8.8% | T300P (ACG→CCG) | yjjU → | putative patatin‑like family phospholipase |
| RA | 4,604,138 | A→G | 5.8% | intergenic (+61/+359) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,397 | G→A | 5.1% | intergenic (+320/+100) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 373849 | 375102 | 1254 | 174 [171] | [170] 173 | frmA–[frmR] | frmA,[frmR] |
| * | * | ÷ | CP009273 | 4100611 | 4101521 | 911 | 173 [168] | [169] 173 | [cdh]–tpiA | [cdh],tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 170 (0.650) | 145 (0.560) | 90/276 | NT | 46.0% | 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) | 6660 (27.090) +TTAATTAA |
194/260 | NT | 96.7% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 361823 | 242 (0.930) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
| * | ? | CP009273 | 360652 = | 251 (0.960) | 6313 (36.400) +46 bp |
181/184 | NT | 97.6% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 1317577 | 217 (0.830) | coding (101/882 nt) | yciV | PHP domain protein | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 18 (0.070) | 14/276 | NT | 7.9% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 566411 = | 211 (0.810) | coding (63/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | = 378046 | NA (NA) | 19 (0.070) | 18/276 | NT | 8.2% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 566415 | 214 (0.820) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | 777033 = | 190 (0.730) | 58 (0.220) +G |
9/274 | NT | 24.5% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | CP009273 | = 2514488 | 171 (0.650) | noncoding (216/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | 1089701 = | NA (NA) | 7 (0.030) | 5/276 | NT | NA | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | CP009273 | = 1427905 | NA (NA) | coding (27/591 nt) | pinR | Rac prophage; putative site‑specific recombinase | |||||
| * | ? | CP009273 | 1203246 = | 37 (0.140) | 164 (0.710) | 98/244 | NT | 79.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 53 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 44 (0.170) | 182 (0.790) | 104/244 | NT | 79.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 53 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2007609 | 241 (0.920) | 33 (0.130) | 24/264 | NT | 14.0% | coding (900/1659 nt) | fliF | flagellar basal‑body MS‑ring and collar protein |
| ? | CP009273 | 2021385 = | 176 (0.700) | coding (114/1695 nt) | yedQ | putative membrane‑anchored diguanylate cyclase | |||||
| * | ? | CP009273 | 4532499 = | 241 (0.920) | 13 (0.050) | 9/258 | NT | 5.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 266 (1.090) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 241 (0.920) | 13 (0.050) | 9/258 | NT | 5.0% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 266 (1.090) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||