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 | 45,545 | A→T | 9.6% | K28M (AAG→ATG) | fixX → | putative ferredoxin FixX |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 151,519 | A→C | 7.9% | I27M (ATT→ATG) | yadK ← | putative fimbrial protein YadK |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 386,844 | T→A | 11.4% | L213Q (CTG→CAG) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 449,135 | C→A | 100% | V503L (GTA→TTA) | cyoB ← | cytochrome bo3 ubiquinol oxidase subunit 1 |
| RA | 454,891 | G→T | 100% | intergenic (+102/‑242) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 461,010 | C→A | 100% | T708N (ACT→AAT) | lon → | Lon protease |
| RA | 594,950 | T→G | 11.2% | H165P (CAT→CCT) | 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 | 771,453 | T→G | 53.7% | intergenic (+842/‑5) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 786,614 | T→G | 10.3% | C328G (TGC→GGC) | aroG → | 3‑deoxy‑7‑phosphoheptulonate synthase, Phe‑sensitive |
| RA | 986,410 | A→C | 8.9% | S191S (TCT→TCG) | ompF ← | outer membrane porin F |
| RA | 1,041,937 | T→G | 11.4% | intergenic (+22/+93) | appA → / ← etk | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase/protein‑tyrosine kinase Etk |
| RA | 1,113,546 | T→A | 14.0% | intergenic (+140/‑33) | opgH → / → yceK | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H/DUF1375 domain‑containing lipoprotein YceK |
| RA | 1,190,446 | A→G | 10.6% | M1T (ATG→ACG) † | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,226,832 | T→G | 11.0% | F78C (TTT→TGT) | ycgJ → | PF05666 family protein YcgJ |
| RA | 1,226,835 | C→A | 11.8% | T79K (ACA→AAA) | ycgJ → | PF05666 family protein YcgJ |
| RA | 1,233,154 | T→A | 8.0% | intergenic (‑124/+22) | dsbB ← / ← nhaB | protein thiol:quinone oxidoreductase DsbB/Na(+):H(+) antiporter NhaB |
| RA | 1,233,157 | T→A | 8.5% | intergenic (‑127/+19) | dsbB ← / ← nhaB | protein thiol:quinone oxidoreductase DsbB/Na(+):H(+) antiporter NhaB |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,541,077 | G→C | 14.0% | A505G (GCC→GGC) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,620,224 | C→G | 9.6% | intergenic (+17/+14) | marB → / ← eamA | multiple antibiotic resistance protein/cysteine/O‑acetylserine exporter EamA |
| RA | 1,620,227 | C→G | 9.7% | intergenic (+20/+11) | marB → / ← eamA | multiple antibiotic resistance protein/cysteine/O‑acetylserine exporter EamA |
| RA | 1,642,370 | C→G | 11.9% | intergenic (+159/+119) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,642,373 | C→G | 11.9% | intergenic (+162/+116) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,674,958 | A→T | 9.4% | intergenic (+11/+14) | tqsA → / ← pntB | autoinducer 2 exporter/pyridine nucleotide transhydrogenase subunit beta |
| RA | 1,778,375 | A→G | 12.4% | intergenic (+28/+15) | ydiO → / ← ydiP | putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator YdiP |
| RA | 1,834,846 | T→C | 9.9% | R13R (CGT→CGC) | ydjZ → | DedA family protein YdjZ |
| 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 | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,589,122 | G→A | 10.4% | G510S (GGC→AGC) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,589,125 | T→C | 9.9% | F511L (TTT→CTT) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,704,306 | A→T | 7.9% | intergenic (‑243/+29) | rnc ← / ← lepB | RNase III/signal peptidase I |
| RA | 2,704,308 | C→T | 7.6% | intergenic (‑245/+27) | rnc ← / ← lepB | RNase III/signal peptidase I |
| RA | 2,761,620 | T→G | 12.6% | K641Q (AAG→CAG) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,264,056 | A→G | 10.1% | I321T (ATC→ACC) | tdcC ← | threonine/serine:H(+) symporter |
| RA | 3,332,822 | G→A | 8.2% | intergenic (‑87/+40) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,332,823 | T→C | 8.2% | intergenic (‑88/+39) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,340,191 | G→A | 7.6% | intergenic (‑126/‑84) | mlaF ← / → yrbG | intermembrane phospholipid transport system, ATP binding subunit MlaF/putative transport protein YrbG |
| RA | 3,473,615 | C→T | 50.2% | W156* (TGG→TAG) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,477,878 | T→A | 10.2% | intergenic (+20/+29) | slyX → / ← slyD | protein SlyX/FKBP‑type peptidyl‑prolyl cis‑trans isomerase SlyD |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,798,235 | A→T | 9.8% | intergenic (+28/+4) | waaL → / ← waaU | O‑antigen ligase/putative ADP‑heptose:LPS heptosyltransferase 4 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,959,515 | T→A | 21.6% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase (NADP(+))/peptidyl‑prolyl cis‑trans isomerase C |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 40.6% | 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 | 4,365,034 | T→A | 8.9% | Q3H (CAA→CAT) N108I (AAC→ATC) |
dsbD ← cutA ← |
protein disulfide oxidoreductase ‑ DsbDreduced copper binding protein CutA |
| RA | 4,376,822 | A→T | 13.3% | intergenic (+123/‑53) | ecnB → / → gdx | bacteriolytic entericidin B lipoprotein/guanidinium exporter |
| RA | 4,439,845 | T→A | 11.5% | intergenic (+52/+27) | ytfK → / ← ytfL | DUF1107 domain‑containing protein YtfK/putative inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2066259–2066619 | 2066619 | 1–361 | 17 [15] | [14] 17 | [insH‑6] | [insH‑6] |
| * | * | ÷ | NC_000913 | 3423752–3424544 | 3424544 | 1–793 | 16 [15] | [15] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 103078 | 46 (1.150) | 4 (0.100) | 4/254 | NT | 8.8% | coding (846/921 nt) | ddlB | D‑alanine‑‑D‑alanine ligase B |
| ? | NC_000913 | = 103096 | 39 (1.020) | coding (864/921 nt) | ddlB | D‑alanine‑‑D‑alanine ligase B | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 6 (0.160) | 6/250 | NT | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 225456 = | 0 (0.000) | 4 (0.110) | 4/246 | NT | 100% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 3427056 | NA (NA) | intergenic (‑23/+20) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | = 287080 | 34 (0.850) | 3 (0.080) | 3/254 | NT | 8.4% | coding (292/1611 nt) | yagH | CP4‑6 prophage; putative xylosidase/arabinosidase |
| ? | NC_000913 | = 287086 | 33 (0.860) | coding (298/1611 nt) | yagH | CP4‑6 prophage; putative xylosidase/arabinosidase | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 9 (0.240) | 6/244 | NT | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 3 (0.080) | 3/246 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1925 (48.580) | 256/262 | NT | 97.7% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 45 (1.130) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 45 (1.130) | 7 (0.240) +34 bp |
6/196 | NT | 21.5% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 24 (0.600) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1030584 = | 44 (1.100) | 5 (0.130) | 5/250 | NT | 11.0% | coding (85/330 nt) | tusE | sulfur transfer protein TusE |
| ? | NC_000913 | 1030610 = | 39 (1.030) | coding (59/330 nt) | tusE | sulfur transfer protein TusE | |||||
| * | ? | NC_000913 | = 1069909 | 55 (1.380) | 4 (0.110) | 3/250 | NT | 7.2% | coding (446/495 nt) | rutF | flavin reductase |
| ? | NC_000913 | = 1069921 | 51 (1.350) | coding (434/495 nt) | rutF | flavin reductase | |||||
| * | ? | NC_000913 | 1096988 = | 25 (0.630) | 5 (0.130) | 5/258 | NT | 17.0% | intergenic (+159/+577) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | 1097191 = | NA (NA) | intergenic (+362/+374) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 9 (0.230) | 22 (0.630) | 21/232 | NT | 66.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 14 (0.400) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.230) | 16 (0.460) | 15/232 | NT | 59.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 14 (0.400) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 39 (1.010) | 30/256 | NT | 98.7% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 1 (0.030) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1910819 = | 41 (1.030) | 3 (0.080) | 3/252 | NT | 7.1% | coding (544/1374 nt) | yebQ | putative transporter YebQ |
| ? | NC_000913 | 1910839 = | 39 (1.020) | coding (564/1374 nt) | yebQ | putative transporter YebQ | |||||
| * | ? | NC_000913 | 2380507 = | 28 (0.700) | 3 (0.080) | 3/254 | NT | 10.0% | coding (137/1296 nt) | menF | isochorismate synthase MenF |
| ? | NC_000913 | 2380519 = | 27 (0.700) | coding (125/1296 nt) | menF | isochorismate synthase MenF | |||||
| * | ? | NC_000913 | = 2382550 | 46 (1.150) | 5 (0.130) | 5/248 | NT | 10.1% | intergenic (+25/‑163) | rbn/elaD | ribonuclease BN/protease ElaD |
| ? | NC_000913 | = 2382557 | 46 (1.230) | intergenic (+32/‑156) | rbn/elaD | ribonuclease BN/protease ElaD | |||||
| * | ? | NC_000913 | 2729630 = | NA (NA) | 8 (0.210) | 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 | 2731065 = | 45 (1.130) | 3 (0.080) | 3/256 | NT | 6.4% | noncoding (93/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | = 4035605 | NA (NA) | noncoding (75/1542 nt) | rrsA | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 2731065 = | 45 (1.130) | 7 (0.180) | 5/256 | NT | 21.3% | noncoding (93/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | = 4208221 | 8 (0.210) | noncoding (75/1542 nt) | rrsE | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 2878135 = | 46 (1.150) | 3 (0.080) | 3/250 | NT | 6.7% | intergenic (+517/+434) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| ? | NC_000913 | 2878153 = | 40 (1.060) | intergenic (+535/+416) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 | |||||
| * | ? | NC_000913 | 3498808 = | 47 (1.180) | 4 (0.100) | 3/254 | NT | 9.0% | coding (981/1374 nt) | cysG | siroheme synthase |
| ? | NC_000913 | 3498902 = | 36 (0.940) | coding (1075/1374 nt) | cysG | siroheme synthase | |||||
| * | ? | NC_000913 | 3620131 = | NA (NA) | 3 (0.080) | 3/258 | NT | 100% | coding (940/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620147 = | 0 (0.000) | coding (956/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3735295 | 32 (0.800) | 3 (0.080) | 3/250 | NT | 8.3% | coding (317/1179 nt) | xylR | DNA‑binding transcriptional dual regulator XylR |
| ? | NC_000913 | = 3735302 | 36 (0.950) | coding (324/1179 nt) | xylR | DNA‑binding transcriptional dual regulator XylR | |||||
| * | ? | NC_000913 | = 3760164 | 27 (0.680) | 3 (0.080) | 3/256 | NT | 9.8% | coding (1086/1392 nt) | selA | selenocysteine synthase |
| ? | NC_000913 | = 3760190 | 29 (0.750) | coding (1060/1392 nt) | selA | selenocysteine synthase | |||||
| * | ? | NC_000913 | = 3933714 | 49 (1.230) | 3 (0.080) | 3/250 | NT | 6.0% | coding (364/420 nt) | rbsD | D‑ribose pyranase |
| ? | NC_000913 | = 3933733 | 48 (1.270) | coding (383/420 nt) | rbsD | D‑ribose pyranase | |||||
| * | ? | NC_000913 | = 3944991 | NA (NA) | 4 (0.100) | 3/252 | NT | 25.9% | noncoding (1288/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | = 4038798 | 12 (0.300) | noncoding (1280/2905 nt) | rrlA | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 4240750 | 36 (0.900) | 6 (0.160) | 6/244 | NT | 14.6% | intergenic (+15/+29) | psiE/xylE | putative phosphate starvation‑inducible protein/D‑xylose:H(+) symporter |
| ? | NC_000913 | = 4240758 | 37 (1.000) | intergenic (+23/+21) | psiE/xylE | putative phosphate starvation‑inducible protein/D‑xylose:H(+) symporter | |||||
| * | ? | NC_000913 | 4295949 = | NA (NA) | 4 (0.110) | 4/250 | NT | NA | noncoding (1/37 nt) | other | REP321c |
| ? | NC_000913 | 4295980 = | NA (NA) | noncoding (32/37 nt) | other | REP321c | |||||
| * | ? | NC_000913 | 4343130 = | 37 (0.930) | 3 (0.080) | 3/252 | NT | 7.5% | coding (1220/1356 nt) | melA | alpha‑galactosidase |
| ? | NC_000913 | 4343158 = | 39 (1.020) | coding (1248/1356 nt) | melA | alpha‑galactosidase | |||||