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 | 9,907 | A→C | 10.4% | intergenic (+14/+21) | mog → / ← satP | molybdopterin adenylyltransferase/acetate/succinate:H(+) symporter |
| RA | 9,908 | G→T | 7.1% | intergenic (+15/+20) | mog → / ← satP | molybdopterin adenylyltransferase/acetate/succinate:H(+) symporter |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 349,717 | T→C | 13.4% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 454,853 | T→C | 6.4% | intergenic (+64/‑280) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,856 | G→A | 6.6% | intergenic (+67/‑277) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 459,834 | C→A | 100% | A316E (GCG→GAG) | lon → | Lon protease |
| RA | 475,971 | C→G | 9.4% | intergenic (+20/+11) | ybaY → / ← atl | PF09619 family lipoprotein YbaY/DNA base‑flipping protein |
| RA | 475,972 | C→G | 9.4% | intergenic (+21/+10) | ybaY → / ← atl | PF09619 family lipoprotein YbaY/DNA base‑flipping protein |
| RA | 594,946 | C→A | 8.0% | Q166H (CAG→CAT) ‡ | cusR ← | DNA‑binding transcriptional activator CusR |
| RA | 594,948 | G→C | 7.7% | Q166E (CAG→GAG) ‡ | cusR ← | DNA‑binding transcriptional activator CusR |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 781,668 | C→T | 12.0% | intergenic (+16/‑417) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 781,670 | A→T | 11.4% | intergenic (+18/‑415) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 781,672 | A→G | 15.0% | intergenic (+20/‑413) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,232,481 | C→T | 5.9% | intergenic (+27/+19) | umuC → / ← dsbB | DNA polymerase V catalytic protein/protein thiol:quinone oxidoreductase DsbB |
| RA | 1,232,484 | A→G | 5.8% | intergenic (+30/+16) | umuC → / ← dsbB | DNA polymerase V catalytic protein/protein thiol:quinone oxidoreductase DsbB |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,407,076 | A→T | 9.6% | T240T (ACT→ACA) | dgcM ← | diguanylate cyclase DgcM |
| RA | 1,440,791 | C→T | 100% | intergenic (‑7/‑267) | ydbK ← / → ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ |
| RA | 1,479,343 | G→T | 10.6% | R69L (CGA→CTA) ‡ | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,479,344 | A→C | 12.7% | R69R (CGA→CGC) ‡ | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,895,391 | A→T | 11.6% | K196I (AAA→ATA) ‡ | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,895,392 | A→T | 12.0% | K196N (AAA→AAT) ‡ | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,934,874 | T→A | 89.1% | T481S (ACC→TCC) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,229,322 | C→G | 10.3% | intergenic (+257/+116) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,229,323 | C→G | 9.3% | intergenic (+258/+115) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,376,867 | T→C | 5.4% | V242V (GTA→GTG) | menH ← | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| RA | 2,425,968 | T→G | 8.4% | intergenic (‑52/+38) | hisQ ← / ← hisJ | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ/histidine ABC transporter periplasmic binding protein |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,672,639 | A→C | 7.1% | Q198P (CAG→CCG) ‡ | hcaD → | putative 3‑phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit |
| RA | 2,672,640 | G→T | 6.8% | Q198H (CAG→CAT) ‡ | hcaD → | putative 3‑phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit |
| RA | 2,724,095 | C→A | 7.3% | intergenic (+13/‑33) | pssA → / → yfiM | phosphatidylserine synthase/protein YfiM |
| RA | 2,724,097 | T→A | 7.9% | intergenic (+15/‑31) | pssA → / → yfiM | phosphatidylserine synthase/protein YfiM |
| RA | 2,724,099 | T→G | 7.6% | intergenic (+17/‑29) | pssA → / → yfiM | phosphatidylserine synthase/protein YfiM |
| RA | 2,767,667 | T→G | 10.1% | intergenic (+312/‑43) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,767,670 | C→A | 8.9% | intergenic (+315/‑40) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,910,100 | C→T | 12.1% | D196N (GAC→AAC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,934,086 | A→G | 6.2% | intergenic (‑398/‑149) | fucA ← / → fucP | L‑fuculose‑phosphate aldolase/L‑fucose:H(+) symporter |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,143,816 | G→T | 6.3% | P117T (CCG→ACG) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,440,147 | G→A | 83.8% | L295F (CTT→TTT) | rpoA ← | RNA polymerase subunit alpha |
| RA | 3,473,615 | C→T | 100% | W156* (TGG→TAG) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,587,225 | A→T | 7.3% | M95L (ATG→TTG) | yhhA → | DUF2756 domain‑containing protein YhhA |
| RA | 3,711,031 | G→A | 100% | P326L (CCG→CTG) | yhjX ← | putative pyruvate transporter |
| RA | 3,754,704 | A→T | 7.8% | intergenic (‑276/+269) | yiaW ← / ← aldB | DUF3302 domain‑containing protein YiaW/aldehyde dehydrogenase B |
| RA | 3,781,051 | C→G | 6.7% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,877,558 | G→C | 5.1% | intergenic (‑93/+147) | yidB ← / ← gyrB | conserved protein YidB/DNA gyrase subunit B |
| RA | 3,991,335 | T→A | 7.3% | I61I (ATT→ATA) | cyaA → | adenylate cyclase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,033,595 | C→A | 100% | P151T (CCT→ACT) | trkH → | K(+) transporter TrkH |
| RA | 4,060,261 | G→T | 7.9% | intergenic (+31/‑186) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,060,264 | A→C | 8.7% | intergenic (+34/‑183) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,230 | C→T | 14.3% | intergenic (‑131/+102) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 34.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,335,654 | T→A | 5.1% | intergenic (‑64/+40) | eptA ← / ← adiC | phosphoethanolamine transferase EptA/arginine:agmatine antiporter |
| RA | 4,365,453 | A→C | 8.2% | intergenic (‑97/+19) | cutA ← / ← dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA |
| RA | 4,548,400 | G→A | 12.1% | C39Y (TGT→TAT) ‡ | fimG → | type 1 fimbriae minor subunit FimG |
| RA | 4,548,401 | T→C | 12.1% | C39C (TGT→TGC) ‡ | fimG → | type 1 fimbriae minor subunit FimG |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196266 | 1211475 | 15210 | 25 [22] | [23] 24 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 2818118–2818144 | 2818251–2818205 | 62–134 | 24 [23] | [23] 24 | [argZ]–[argY] | [argZ],[argY] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315646 | NA (NA) | 5 (0.100) | 4/254 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315843 = | NA (NA) | 5 (0.090) | 4/258 | NT | NA | noncoding (615/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315886 = | NA (NA) | noncoding (658/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315852 | NA (NA) | 18 (0.340) | 9/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316093 | NA (NA) | 6 (0.110) | 5/258 | NT | NA | noncoding (865/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316135 | NA (NA) | noncoding (907/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 4 (0.080) | 4/246 | NT | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 471875 | 54 (0.990) | 5 (0.100) | 3/254 | NT | 8.8% | coding (1240/1782 nt) | mdlB | ABC transporter family protein MdlB |
| ? | NC_000913 | = 471894 | 52 (1.000) | coding (1259/1782 nt) | mdlB | ABC transporter family protein MdlB | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2288 (42.440) | 254/262 | NT | 97.8% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 52 (0.960) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 52 (0.960) | 15 (0.370) +34 bp |
11/196 | NT | 33.1% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 30 (0.550) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1345576 = | 44 (0.810) | 3 (0.060) | 3/254 | NT | 6.6% | coding (1167/1986 nt) | pdeR | cyclic di‑GMP phosphodiesterase PdeR |
| ? | NC_000913 | 1345622 = | 42 (0.800) | coding (1121/1986 nt) | pdeR | cyclic di‑GMP phosphodiesterase PdeR | |||||
| * | ? | NC_000913 | 2727891 = | NA (NA) | 10 (0.190) | 5/252 | NT | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 2729630 = | NA (NA) | 9 (0.170) | 8/254 | NT | NA | noncoding (1528/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2729652 = | NA (NA) | noncoding (1506/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 2808593 | 44 (0.810) | 3 (0.060) | 3/250 | NT | 6.6% | pseudogene (278/1178 nt) | ygaY | putative transporter YgaY, N‑terminal fragment |
| ? | NC_000913 | = 2808601 | 43 (0.840) | pseudogene (286/1178 nt) | ygaY | putative transporter YgaY, N‑terminal fragment | |||||