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 | 11.6% | intergenic (+14/+21) | mog → / ← satP | molybdopterin adenylyltransferase/acetate/succinate:H(+) symporter |
| RA | 9,908 | G→T | 10.6% | intergenic (+15/+20) | mog → / ← satP | molybdopterin adenylyltransferase/acetate/succinate:H(+) symporter |
| RA | 83,587 | A→C | 8.0% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 7.6% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 324,318 | G→A | 6.8% | A187A (GCG→GCA) | ykgG → | DUF162 domain‑containing lactate utilization protein YkgG |
| RA | 475,972 | C→G | 14.6% | intergenic (+21/+10) | ybaY → / ← atl | PF09619 family lipoprotein YbaY/DNA base‑flipping protein |
| RA | 481,225 | T→G | 12.7% | intergenic (‑517/+29) | tomB ← / ← acrB | protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB |
| RA | 481,228 | C→A | 10.5% | intergenic (‑520/+26) | tomB ← / ← acrB | protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 887,392 | T→A | 8.6% | intergenic (‑53/‑31) | ybjJ ← / → rcdA | inner membrane protein YbjJ/DNA‑binding transcriptional regulator RcdA |
| RA | 887,393 | T→A | 10.6% | intergenic (‑54/‑30) | ybjJ ← / → rcdA | inner membrane protein YbjJ/DNA‑binding transcriptional regulator RcdA |
| RA | 1,018,983 | A→T | 11.8% | intergenic (+46/+30) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,018,986 | A→T | 12.5% | intergenic (+49/+27) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,196,220 | C→T | 45.6% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 43.5% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 47.4% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 41.0% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | 38.2% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | 37.4% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | 37.6% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | 34.5% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | 24.3% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,286,793 | A→G | 16.8% | K29E (AAG→GAG) | ychS → | putative uncharacterized protein YchS |
| 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 | 1,928,799 | A→C | 9.0% | L14R (CTT→CGT) | ptrB ← | oligopeptidase B |
| RA | 1,928,802 | G→T | 9.0% | T13K (ACG→AAG) | ptrB ← | oligopeptidase B |
| 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 | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,761,620 | T→G | 10.7% | K641Q (AAG→CAG) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,814,174 | T→A | 11.7% | intergenic (+20/+44) | emrB → / ← luxS | multidrug efflux pump membrane subunit EmrB/S‑ribosylhomocysteine lyase |
| RA | 2,814,175 | T→A | 11.6% | intergenic (+21/+43) | emrB → / ← luxS | multidrug efflux pump membrane subunit EmrB/S‑ribosylhomocysteine lyase |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,404,619 | A→G | 9.6% | intergenic (+161/‑817) | yhdH → / → accB | acrylyl‑CoA reductase/biotin carboxyl carrier protein |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,831,761 | C→G | 10.7% | A435A (GCC→GCG) | yicH → | AsmA famly protein YicH |
| RA | 3,915,227 | G→T | 10.7% | intergenic (‑27/+326) | glmU ← / ← atpC | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase/ATP synthase F1 complex subunit epsilon |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,125,097 | C→T | 69.4% | E572K (GAG→AAG) | priA ← | primosome factor N' |
| RA | 4,177,171 | T→A | 9.3% | intergenic (+43/‑187) | tufB → / → secE | translation elongation factor Tu 2/Sec translocon subunit SecE |
| RA | 4,177,172 | T→A | 10.0% | intergenic (+44/‑186) | tufB → / → secE | translation elongation factor Tu 2/Sec translocon subunit SecE |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 35.5% | 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 | 4,321,246 | A→G | 10.0% | M1T (ATG→ACG) † *151R (TGA→CGA) |
phnH ← phnG ← |
carbon‑phosphorus lyase core complex subunit PhnH carbon‑phosphorus lyase core complex subunit PhnG |
| RA | 4,376,280 | G→A | 8.0% | intergenic (+15/‑37) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,376,291 | T→C | 8.6% | intergenic (+26/‑26) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,520,500 | Δ1 bp | 8.0% | intergenic (‑176/+171) | yjhU ← / ← yjhF | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU/KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,520,504:1 | +T | 8.2% | intergenic (‑180/+167) | yjhU ← / ← yjhF | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU/KpLE2 phage‑like element; putative transporter YjhF |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366077 | 366411 | 335 | 14 [13] | [13] 14 | [lacZ] | [lacZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315413 | NA (NA) | 4 (0.110) | 4/238 | NT | NA | noncoding (185/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315613 | NA (NA) | noncoding (385/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315563 = | NA (NA) | 8 (0.210) | 7/244 | NT | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315642 | NA (NA) | 6 (0.150) | 5/260 | NT | NA | noncoding (414/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315712 | NA (NA) | noncoding (484/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315781 = | NA (NA) | 5 (0.130) | 5/254 | NT | NA | noncoding (553/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315875 = | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315852 | NA (NA) | 52 (1.300) | 13/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315892 = | NA (NA) | 6 (0.150) | 5/258 | NT | NA | noncoding (664/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315923 = | NA (NA) | noncoding (695/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 316193 = | NA (NA) | 4 (0.100) | 3/246 | NT | NA | noncoding (965/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 316230 = | NA (NA) | noncoding (1002/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 382211 | NA (NA) | 6 (0.150) | 5/254 | NT | NA | noncoding (952/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382218 | NA (NA) | noncoding (959/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 427762 | 50 (1.210) | 3 (0.080) | 3/250 | NT | 6.1% | coding (116/1848 nt) | secD | Sec translocon accessory complex subunit SecD |
| ? | NC_000913 | = 427779 | 45 (1.150) | coding (133/1848 nt) | secD | Sec translocon accessory complex subunit SecD | |||||
| * | ? | NC_000913 | 474269 = | NA (NA) | 3 (0.080) | 3/252 | NT | NA | intergenic (+17/+32) | amtB/tesB | ammonia/ammonium transporter/acyl‑CoA thioesterase II |
| ? | NC_000913 | 474296 = | NA (NA) | intergenic (+44/+5) | amtB/tesB | ammonia/ammonium transporter/acyl‑CoA thioesterase II | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 3391 (82.570) | 261/262 | NT | 99.0% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 34 (0.820) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 566841 | 12 (0.290) | 7 (0.230) +34 bp |
7/196 | NT | 29.1% | noncoding (65/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 34 (0.820) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 909154 | 34 (0.820) | 3 (0.080) | 3/254 | NT | 7.6% | coding (141/1002 nt) | ltaE | low‑specificity L‑threonine aldolase |
| ? | NC_000913 | = 909188 | 40 (1.000) | coding (107/1002 nt) | ltaE | low‑specificity L‑threonine aldolase | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.070) | 5 (0.140) | 5/232 | NT | 68.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 2 (0.060) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1561749 | 30 (0.720) | 3 (0.080) | 3/252 | NT | 9.9% | coding (733/1551 nt) | ddpA | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1561763 | 26 (0.660) | coding (719/1551 nt) | ddpA | putative D,D‑dipeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2321967 | 33 (0.800) | 4 (0.100) | 4/252 | NT | 11.2% | coding (102/1386 nt) | atoC | DNA‑binding transcriptional activator/ornithine decarboxylase inhibitor AtoC |
| ? | NC_000913 | = 2321976 | 32 (0.810) | coding (111/1386 nt) | atoC | DNA‑binding transcriptional activator/ornithine decarboxylase inhibitor AtoC | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 4 (0.100) | 4/252 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3883262 = | 38 (0.920) | 3 (0.080) | 3/252 | NT | 7.7% | coding (468/1404 nt) | dnaA | chromosomal replication initiator protein DnaA |
| ? | NC_000913 | 3883286 = | 36 (0.910) | coding (444/1404 nt) | dnaA | chromosomal replication initiator protein DnaA | |||||
| * | ? | NC_000913 | = 4040683 | 45 (1.090) | 8 (0.200) | 4/260 | NT | 14.9% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein |
| ? | NC_000913 | = 4213162 | 47 (1.150) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||
| * | ? | NC_000913 | = 4162839 | 52 (1.260) | 3 (0.080) | 3/250 | NT | 5.8% | coding (432/1101 nt) | trmA | tRNA m(5)U54 methyltransferase |
| ? | NC_000913 | = 4162849 | 49 (1.250) | coding (422/1101 nt) | trmA | tRNA m(5)U54 methyltransferase | |||||
| * | ? | NC_000913 | = 4296067 | NA (NA) | 3 (0.080) | 3/250 | NT | NA | noncoding (6/37 nt) | other | REP321e |
| ? | NC_000913 | = 4296086 | NA (NA) | noncoding (25/37 nt) | other | REP321e | |||||