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 | 107,554 | G→T | 14.5% | intergenic (+80/‑151) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 164,581 | A→C | 17.4% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 238,507 | G→T | 7.8% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 238,535 | G→T | 6.8% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 287,925 | A→C | 5.0% | Q379H (CAA→CAC) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 357,775 | A→T | 5.5% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 380,005 | A→C | 8.7% | intergenic (‑124/+64) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 656,771 | A→C | 5.8% | N72T (AAC→ACC) | pagP → | phospholipid:lipid A palmitoyltransferase |
| RA | 777,208 | A→C | 6.7% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 781,254 | A→T | 5.2% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 843,216 | G→T | 9.8% | M295I (ATG→ATT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 863,966 | A→C | 8.1% | T109P (ACC→CCC) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 1,287,122 | T→G | 11.3% | noncoding (115/171 nt) R19R (AGG→CGG) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,124 | C→A | 6.7% | noncoding (113/171 nt) R18L (CGC→CTC) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,143 | G→T | 5.5% | noncoding (94/171 nt) P12T (CCA→ACA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,149 | G→A | 8.2% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,351,227 | A→C | 6.5% | intergenic (‑188/+180) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,351,228 | G→C | 10.1% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,399,240 | C→G | 16.4% | G96A (GGC→GCC) | fnr ← | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor |
| RA | 1,630,528 | T→G | 10.7% | Y129S (TAT→TCT) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,708,709 | T→A | 9.0% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→A | 11.2% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 5.2% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,720,364 | G→T | 8.3% | intergenic (+21/+26) | slyB → / ← slyA | outer membrane lipoprotein/global transcriptional regulator |
| RA | 1,864,768 | T→C | 6.8% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,177,234 | C→A | 11.4% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 12.9% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,229,177 | A→C | 10.1% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,304,649 | C→T | 11.8% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,680 | T→C | 6.3% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,762 | T→C | 7.1% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,085 | A→G | 6.2% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 5.7% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 5.7% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,454,266 | C→A | 7.9% | pseudogene (736/2646 nt) | yfcU ← | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,470,427 | C→A | 15.9% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,431 | G→T | 8.6% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,436 | C→A | 12.5% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,718,314 | A→C | 5.2% | V72G (GTT→GGT) | yfiF ← | putative methyltransferase |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,947,470 | A→T | 5.6% | intergenic (+7/‑27) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,046,050 | T→G | 6.7% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,054,888 | A→T | 7.9% | V186E (GTA→GAA) | ygfB ← | UPF0149 family protein |
| RA | 3,087,396 | T→G | 8.0% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,239,609 | T→G | 7.4% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,269,956 | T→C | 6.5% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,423,531 | T→G | 6.5% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,440,923 | C→A | 100% | G36V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,504,880 | A→C | 6.6% | intergenic (+97/+55) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,537,327 | G→T | 5.5% | intergenic (+39/‑58) | greB → / → yhgF | transcript cleavage factor/putative transcriptional accessory protein |
| RA | 3,539,659 | A→C | 6.2% | S759R (AGC→CGC) | yhgF → | putative transcriptional accessory protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,608,695 | C→G | 8.8% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,728,120 | T→G | 5.8% | T418P (ACG→CCG) | xylB ← | xylulokinase |
| RA | 3,728,125 | T→G | 7.7% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,781,022 | T→G | 7.6% | intergenic (+5/‑193) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,032 | T→A | 15.4% | intergenic (+15/‑183) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,050 | T→A | 14.3% | intergenic (+33/‑165) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,067 | T→G | 6.0% | intergenic (+50/‑148) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,092 | T→A | 5.3% | intergenic (+75/‑123) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,158 | A→C | 5.1% | intergenic (+141/‑57) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,828,980 | A→C | 7.5% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,913,021 | A→T | 5.1% | T216T (ACT→ACA) | glmS ← | L‑glutamine:D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,959,457 | T→G | 5.4% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,482 | A→C | 7.3% | intergenic (+37/+50) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 9.1% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,998,056 | T→G | 6.0% | L25R (CTT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,023,452 | A→T | 5.7% | K239N (AAA→AAT) | tatC → | TatABCE protein translocation system subunit |
| RA | 4,048,768 | A→C | 6.9% | K601N (AAA→AAC) | polA → | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease |
| RA | 4,051,262 | A→C | 5.0% | noncoding (227/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,095,965 | T→G | 5.6% | E6D (GAA→GAC) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,296,060 | C→T | 26.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,948 | A→G | 6.0% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,520,500 | Δ1 bp | 5.3% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 5.2% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,559,335 | A→C | 5.8% | F64L (TTT→TTG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,614,378 | A→G | 5.2% | intergenic (+118/+302) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,633,743 | C→T | 100% | M1M (ATG→ATA) † | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 772997 | 774215 | 1219 | 213 [207] | [208] 210 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037681 | 1039317 | 1637 | 210 [205] | [207] 210 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 1166026 | 1167436 | 1411 | 210 [209] | [208] 217 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423743–3424543 | 3424543 | 1–801 | 210 [205] | [207] 212 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274620 = | NA (NA) | 10 (0.020) | 7/258 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 781222 | 337 (0.620) | 18 (0.040) | 8/240 | NT | 5.4% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 2521485 = | 340 (0.720) | intergenic (+157/+108) | lysV/xapR | tRNA‑Lys/transcriptional activator of xapAB | |||||
| * | ? | NC_000913 | 781369 = | 359 (0.660) | 54 (0.100) +GAAG |
19/268 | NT | 13.6% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 346 (0.640) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 781652 | 265 (0.490) | 29 (0.070) +33 bp |
4/210 | NT | 11.7% | noncoding (76/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | 2521253 = | 312 (0.570) | noncoding (1/76 nt) | lysV | tRNA‑Lys | |||||
| * | ? | NC_000913 | 1207790 = | 198 (0.360) | 186 (0.390) | 101/244 | NT | 49.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 198 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 191 (0.350) | 252 (0.520) | 121/244 | NT | 57.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 198 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1287084 | 203 (0.370) | 21 (0.050) | 17/236 | NT | 8.3% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | NC_000913 | 1287557 = | 289 (0.620) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 393 (0.740) | 151/268 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2466384 | 544 (1.000) | 76 (0.160) | 51/244 | NT | 13.8% | intergenic (+1/‑161) | argW/intS | tRNA‑Arg/CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase |
| ? | NC_000913 | 2476600 = | 472 (0.980) | intergenic (+2/+94) | pawZ/dsdC | tRNA‑OTHER/dsd operon activator; autorepressor | |||||
| * | ? | NC_000913 | = 2618037 | NA (NA) | 5 (0.010) | 4/264 | NT | NA | intergenic (+100/+38) | yfgD/hda | putative oxidoreductase/ATPase regulatory factor involved in DnaA inactivation |
| ? | NC_000913 | = 2618053 | NA (NA) | intergenic (+116/+22) | yfgD/hda | putative oxidoreductase/ATPase regulatory factor involved in DnaA inactivation | |||||
| * | ? | NC_000913 | 2700550 = | 409 (0.750) | 23 (0.050) | 13/238 | NT | 6.6% | noncoding (31/77 nt) | ohsC | sRNA antisense regulator of shoB toxin |
| ? | NC_000913 | 2700601 = | 303 (0.650) | intergenic (+5/+17) | ohsC/acpS | sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1 | |||||
| * | ? | NC_000913 | = 2817942 | 328 (0.600) | 19 (0.040) | 14/236 | NT | 5.7% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 345 (0.740) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 3255287 | NA (NA) | 8 (0.020) | 6/264 | NT | NA | noncoding (71/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 3255319 | NA (NA) | noncoding (103/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 3620350 | NA (NA) | 7 (0.010) | 5/264 | NT | 100% | coding (1159/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3620425 | 0 (0.000) | coding (1234/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||