mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.7 revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_007779 | 63,992 | G→A | H597Y (CAT→TAT) | polB ← | DNA polymerase II |
| RA | NC_007779 | 64,108 | G→T | S558* (TCG→TAG) | polB ← | DNA polymerase II |
| RA | NC_007779 | 66,528 | T→C | Q8R (CAG→CGG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase |
| MC JC | NC_007779 | 66,533 | 3540 bp→27 bp | [araD]–araB | [araD], araA, araB | |
| RA | NC_007779 | 70,289 | G→T | intergenic (‑241/‑98) | araB ← / → araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| RA | NC_007779 | 365,743 | G→A | A331V (GCG→GTG) | lacI ← | DNA‑binding transcriptional repressor |
| RA | NC_007779 | 502,653 | C→T | intergenic (‑191/+47) | ybaL ← / ← fsr | transporter with NAD(P)‑binding Rossmann‑fold domain/fosmidomycin efflux system |
| RA | NC_007779 | 547,694 | A→G | intergenic (+123/‑1156) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein |
| RA | NC_007779 | 547,835 | +G | intergenic (+264/‑1015) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein |
| RA | NC_007779 | 649,229 | A→T | L162H (CTC→CAC) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| MC JC | NC_007779 | 654,214 | Δ1,199 bp | insH | insH | |
| RA | NC_007779 | 705,435 | T→C | L357S (TTG→TCG) | nagE → | fused N‑acetyl glucosamine‑specific PTS enzyme IICBA components |
| RA | NC_007779 | 1,093,686 | T→C | V130A (GTA→GCA) | ycdT → | diguanylate cyclase |
| MC JC | NC_007779 | 1,105,622 | Δ1,336 bp | insD–insC | insD, insC | |
| RA | NC_007779 | 1,145,280 | A→G | L222S (TTA→TCA) | rne ← | fused ribonucleaseE endoribonuclease and scaffold for formation of degradosome |
| RA | NC_007779 | 1,246,924 | 2 bp→AA | coding (188‑189/441 nt) | ycgY → | hypothetical protein |
| MC JC | NC_007779 | 1,301,041 | Δ1,336 bp | insC–insD | insC, insD | |
| RA | NC_007779 | 1,452,268 | G→A | L266L (CTG→TTG) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | NC_007779 | 1,778,780 | G→A | D494N (GAT→AAT) | ydiF → | fused acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit and beta subunit |
| MC JC | NC_007779 | 1,980,209 | Δ1,199 bp | insH | insH | |
| RA | NC_007779 | 2,034,560 | A→G | V219V (GTT→GTC) | yedJ ← | phosphohydrolase |
| MC JC | NC_007779 | 2,176,983 | Δ1,199 bp | insH | insH | |
| MC JC | NC_007779 | 2,320,795 | Δ1,336 bp | insD–insC | insD, insC | |
| MC JC | NC_007779 | 2,411,459 | Δ776 bp | insB–insA | insB, insA | |
| RA | NC_007779 | 2,842,666 | G→T | R67R (CGC→CGA) | hycG ← | hydrogenase 3 and formate hydrogenase complex, HycG subunit |
| RA | NC_007779 | 2,866,111 | A→G | intergenic (‑21/+159) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/outer membrane lipoprotein |
| RA | NC_007779 | 3,109,077 | C→A | noncoding (56/76 nt) | pheV → | tRNA‑Phe |
| MC JC | NC_007779 | 3,261,134 | Δ1,199 bp | insH–[tdcD] | insH, [tdcD] | |
| RA | NC_007779 | 3,374,780 | G→A | L19L (CTG→CTA) | dcuD → | transporter |
| RA | NC_007779 | 3,472,558 | G→C | A162G (GCA→GGA) | btuB ← | vitamin B12/cobalamin outer membrane transporter |
| RA | NC_007779 | 3,475,433 | C→A | G61V (GGC→GTC) | fabR ← | DNA‑binding transcriptional repressor |
| MC JC | NC_007779 | 3,539,230 | 3461 bp→29 bp | rhaB–[rhaD] | rhaB, rhaA, [rhaD] | |
| RA | NC_007779 | 3,542,911 | G→A | G168D (GGC→GAC) | rhaD → | rhamnulose‑1‑phosphate aldolase |
| MC JC | NC_007779 | 3,742,936 | Δ1,336 bp | insD–insC | insD, insC | |
| MC JC | NC_007779 | 3,746,911 | Δ1,199 bp | insH | insH | |
| RA | NC_007779 | 4,154,211 | T→G | K29T (AAG→ACG) | crp ← | DNA‑binding transcriptional dual regulator |
| MC JC | NC_007779 | 4,310,363 | Δ1,199 bp | insH–[alsK] | insH, [alsK] | |
| RA | NC_007779 | 4,371,274 | (A)5→3 | intergenic (‑9/+296) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | NC_007779 | 4,479,514 | A→G | intergenic (+117/‑28) | yjgJ → / → yjgK | transcriptional regulator/hypothetical protein |
| RA | NC_007779 | 4,590,160 | G→A | Q446* (CAA→TAA) | hsdR ← | endonuclease R |
| RA | NC_007779 | 4,607,189 | C→T | W117* (TGG→TAG) | yjjP ← | inner membrane protein |
| RA | NC_007779 | 4,621,349 | G→T | L133I (CTA→ATA) | yjjI ← | hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 227064–228688 | 228919–228690 | 3–1856 | 9 [7] | [7] 8 | [rrlH]–rrfH | [rrlH],rrfH |
| * | * | ÷ | NC_007779 | 283070 | 283211 | 142 | 8 [7] | [7] 9 | yagF | dehydratase |
| * | * | ÷ | NC_007779 | 363580 | 365538 | 1959 | 26 [0] | [0] 10 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_007779 | 400318 | 400541 | 224 | 8 [7] | [6] 8 | ddlA/yaiB | D‑alanine‑D‑alanine ligase A/hypothetical protein |
| * | * | ÷ | NC_007779 | 771243 | 771368 | 126 | 8 [6] | [7] 8 | mngB/cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| * | * | ÷ | NC_007779 | 1213625 | 1213745 | 121 | 8 [7] | [6] 8 | elbA/ycgX | hypothetical protein/hypothetical protein |
| * | * | ÷ | NC_007779 | 1531754 | 1532017 | 264 | 8 [7] | [7] 8 | ydcD | hypothetical protein |
| * | * | ÷ | NC_007779 | 1793895 | 1793968 | 74 | 8 [7] | [6] 8 | ydiV/nlpC | hypothetical protein/lipoprotein |
| * | * | ÷ | NC_007779 | 2035889 | 2036168 | 280 | 8 [7] | [7] 8 | yedR/hchA | inner membrane protein/Hsp31 molecular chaperone |
| * | * | ÷ | NC_007779 | 2059681 | 2059844 | 164 | 8 [7] | [7] 8 | [yeeN] | [yeeN] |
| * | * | ÷ | NC_007779 | 2101893 | 2101977 | 85 | 8 [7] | [7] 9 | ugd/gnd | UDP‑glucose 6‑dehydrogenase/gluconate‑6‑phosphate dehydrogenase, decarboxylating |
| * | * | ÷ | NC_007779 | 2410230 | 2410339 | 110 | 9 [7] | [7] 8 | nuoA/lrhA | NADH:ubiquinone oxidoreductase, membrane subunit A/DNA‑binding transcriptional repressor |
| * | * | ÷ | NC_007779 | 2475627 | 2475974 | 348 | 8 [7] | [7] 8 | [yfdI] | [yfdI] |
| * | * | ÷ | NC_007779 | 2526453 | 2526496 | 44 | 9 [0] | [0] 11 | valU/valX | tRNA‑Val/tRNA‑Val |
| * | * | ÷ | NC_007779 | 2787150 | 2787256 | 107 | 8 [7] | [7] 9 | yqaD | hypothetical protein |
| * | * | ÷ | NC_007779 | 3135098 | 3135267 | 170 | 8 [6] | [7] 9 | pitB/gss | phosphate transporter/fused glutathionylspermidine amidase and glutathionylspermidine synthetase |
| * | * | ÷ | NC_007779 | 3268810 | 3269133 | 324 | 8 [7] | [7] 9 | yhaC | hypothetical protein |
| * | * | ÷ | NC_007779 | 3592530 | 3592613 | 84 | 8 [7] | [7] 8 | yihF/dsbA | hypothetical protein/periplasmic protein disulfide isomerase I |
| * | * | ÷ | NC_007779 | 3870490 | 3870785 | 296 | 8 [7] | [7] 8 | yibH/yibG | hypothetical protein/hypothetical protein |
| * | * | ÷ | NC_007779 | 3888401 | 3888533 | 133 | 8 [7] | [6] 8 | [yiaU] | [yiaU] |
| * | * | ÷ | NC_007779 | 4163780 | 4163890 | 111 | 8 [7] | [7] 8 | [fkpA] | [fkpA] |
| * | * | ÷ | NC_007779 | 4184856 | 4185016 | 161 | 8 [7] | [7] 8 | gspC/gspA | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | NC_007779 | 4213650–4216670 | 4216670 | 1–3021 | 8 [7] | [7] 8 | [rrlE]–[rrfE] | [rrlE],[rrfE] |
| * | * | ÷ | NC_007779 | 4307993 | 4308084 | 92 | 9 [7] | [6] 8 | yjcR/yjcS | membrane fusion protein of efflux pump/alkyl sulfatase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 269765 = | NA (NA) | 38 (0.820) | 32/200 | 0.4 | 100% | coding (300/405 nt) | insN | partial regulator of insertion element IS911A |
| ? | NC_007779 | = 370983 | 0 (0.000) | coding (536/882 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase | |||||
| * | ? | NC_007779 | = 279335 | NA (NA) | 27 (0.580) | 26/200 | 0.7 | 100% | coding (252/339 nt) | ykgN | IS protein |
| ? | NC_007779 | 370982 = | 0 (0.000) | coding (535/882 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase | |||||
| * | ? | NC_007779 | = 363579 | 0 (0.000) | 14 (0.510) +41 bp |
12/118 | 1.0 | 100% | coding (1951/3075 nt) | lacZ | beta‑D‑galactosidase |
| ? | NC_007779 | 3464760 = | NA (NA) | intergenic (‑136/+165) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | NC_007779 | 1209367 = | 50 (1.080) | 10 (0.260) | 8/168 | 2.5 | 22.5% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | NC_007779 | 1211196 = | 27 (0.690) | intergenic (‑500/‑66) | tfaE/pin | tail fiber assembly protein/site‑specific DNA recombinase | |||||
| * | ? | NC_007779 | 3464760 = | NA (NA) | 10 (0.240) +AATTAATTCC |
10/180 | 2.2 | 44.2% | intergenic (‑136/+165) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA |
| ? | NC_007779 | = 3464932 | 14 (0.300) | noncoding (113/120 nt) | rrfB | 5S ribosomal RNA | |||||
| * | ? | NC_007779 | = 3750590 | 0 (0.000) | 27 (0.600) | 21/192 | 1.0 | 100% | intergenic (‑104/‑69) | tnaA/insH | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/IS5 element protein |
| ? | NC_007779 | 3751790 = | 0 (0.000) | intergenic (+151/+116) | insH/tnaC | IS5 element protein/tryptophanase leader peptide | |||||