mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 88 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,228,239 | 0 | G | C | 53.8% | 1.3 / 13.5 | 13 | pseudogene (371/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 2,608,244 | 0 | T | G | 40.0% | 56.5 / 10.9 | 55 | V443G (GTG→GGG) | hyfF | hydrogenase 4, membrane subunit |
| * | NC_000913 | 3,862,661 | 0 | T | G | 39.6% | 26.7 / 14.8 | 50 | pseudogene (943/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 2,096,090 | 0 | A | G | 39.1% | 67.8 / 14.6 | 46 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase, catalytic subunit with HisH |
| * | NC_000913 | 3,665,702 | 0 | C | A | 38.7% | 121.1 / 29.3 | 75 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 3,862,670 | 0 | T | A | 38.1% | 17.9 / 17.3 | 50 | pseudogene (934/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 3,862,664 | 0 | C | G | 37.0% | 15.4 / 17.8 | 50 | pseudogene (940/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 3,206,446 | 0 | C | A | 35.4% | 42.9 / 15.9 | 48 | intergenic (‑190/‑17) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 2,332,823 | 0 | A | G | 34.2% | 54.3 / 17.9 | 38 | pseudogene (1580/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| * | NC_000913 | 433,649 | 0 | T | G | 33.9% | 56.5 / 14.2 | 61 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,206,483 | 0 | G | A | 33.3% | 40.5 / 15.0 | 44 | K7K (AAG→AAA) | ttdA | L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 1,876,015 | 0 | A | G | 32.1% | 91.5 / 12.4 | 56 | I115V (ATT→GTT) | yeaN | putative MFS transporter, inner membrane protein |
| * | NC_000913 | 2,386,862 | 0 | G | A | 32.1% | 68.6 / 34.6 | 53 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 3,665,657 | 0 | C | A | 31.9% | 223.6 / 23.4 | 91 | V52L (GTA→TTA) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 954,388 | 0 | C | T | 31.5% | 60.2 / 17.6 | 56 | A27T (GCA→ACA) | focA | formate channel |
| * | NC_000913 | 3,733,280 | 0 | T | A | 31.2% | 94.3 / 17.6 | 48 | N360K (AAT→AAA) | xylG | D‑xylose ABC transporter dual domain ATPase |
| * | NC_000913 | 3,782,919 | 0 | T | A | 31.1% | 41.4 / 12.2 | 53 | D248V (GAT→GTT) | gpsA | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| * | NC_000913 | 345,328 | 0 | C | A | 31.1% | 181.6 / 24.0 | 74 | intergenic (+337/‑76) | yahL/yahM | uncharacterized protein/uncharacterized protein |
| * | NC_000913 | 1,101,673 | 0 | T | A | 31.0% | 119.9 / 11.6 | 59 | L4F (TTA→TTT) | csgG | curli production assembly/transport outer membrane lipoprotein |
| * | NC_000913 | 127,209 | 0 | T | G | 30.9% | 112.4 / 11.4 | 55 | G505G (GGT→GGG) | aceF | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| Marginal new junction evidence (lowest skew 10 of 249 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1125266 | 71 (0.790) | 11 (0.130) | 9/402 | 5.6 | 11.2% | coding (61/1209 nt) | mdtH | multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin |
| ? | NC_000913 | = 1125612 | 107 (1.250) | coding (51/585 nt) | rimJ | ribosomal‑protein‑S5‑alanine N‑acetyltransferase | |||||
| * | ? | NC_000913 | = 4510494 | 113 (1.260) | 8 (0.090) | 7/406 | 6.3 | 6.6% | intergenic (+361/+196) | yjhV/fecE | pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase |
| ? | NC_000913 | = 4510656 | 117 (1.350) | intergenic (+523/+34) | yjhV/fecE | pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase | |||||
| * | ? | NC_000913 | 4240699 = | 92 (1.020) | 8 (0.090) | 7/408 | 6.4 | 8.7% | coding (375/411 nt) | psiE | phosphate starvation inducible protein |
| ? | NC_000913 | 4241011 = | 80 (0.920) | coding (1244/1476 nt) | xylE | D‑xylose transporter | |||||
| * | ? | NC_000913 | 841168 = | 64 (0.710) | 8 (0.090) | 7/412 | 6.4 | 12.3% | coding (364/2283 nt) | fiu | catecholate siderophore receptor |
| ? | NC_000913 | 841458 = | 52 (0.590) | coding (74/2283 nt) | fiu | catecholate siderophore receptor | |||||
| * | ? | NC_000913 | = 123302 | 116 (1.290) | 9 (0.100) | 7/416 | 6.4 | 7.6% | coding (286/2664 nt) | aceE | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| ? | NC_000913 | = 123397 | 103 (1.160) | coding (381/2664 nt) | aceE | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | 2180486 = | 103 (1.150) | 7 (0.080) | 6/396 | 6.6 | 8.0% | coding (392/1005 nt) | yegU | ADP‑ribosylglycohydrolase family protein |
| ? | NC_000913 | 2180910 = | 64 (0.760) | coding (816/1005 nt) | yegU | ADP‑ribosylglycohydrolase family protein | |||||
| * | ? | NC_000913 | 4562073 = | 94 (1.050) | 10 (0.120) | 6/404 | 6.7 | 10.3% | coding (603/1179 nt) | yjiJ | DUF1228 family putative inner membrane MFS superfamily transporter |
| ? | NC_000913 | 4562236 = | 85 (0.990) | coding (440/1179 nt) | yjiJ | DUF1228 family putative inner membrane MFS superfamily transporter | |||||
| * | ? | NC_000913 | 3983571 = | 84 (0.930) | 6 (0.070) | 6/402 | 6.7 | 6.1% | coding (614/1236 nt) | aslB | putative AslA‑specific sulfatase‑maturating enzyme |
| ? | NC_000913 | 3983798 = | 106 (1.240) | coding (841/1236 nt) | aslB | putative AslA‑specific sulfatase‑maturating enzyme | |||||
| * | ? | NC_000913 | 3777891 = | 91 (1.010) | 6 (0.070) | 6/402 | 6.7 | 5.7% | coding (493/1656 nt) | lldP | L‑lactate permease |
| ? | NC_000913 | 3778056 = | 113 (1.320) | coding (658/1656 nt) | lldP | L‑lactate permease | |||||
| * | ? | NC_000913 | = 2926096 | 96 (1.070) | 10 (0.120) | 6/404 | 6.7 | 9.1% | coding (749/849 nt) | queF | 7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent) |
| ? | NC_000913 | = 2926203 | 107 (1.240) | intergenic (+7/‑105) | queF/ygdH | 7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)/UPF0717 family protein | |||||