mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 244 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,606,330 | 1 | . | G | 78.0% | 249.4 / 69.3 | 100 | noncoding (72/87 nt) | leuQ | tRNA‑Leu |
| * | NC_000913 | 3,240,984 | 1 | . | G | 75.2% | 326.9 / 111.6 | 121 | coding (1041/1245 nt) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 380,022 | 0 | G | . | 47.5% | 97.5 / 114.7 | 61 | intergenic (‑141/+47) | frmR/yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| * | NC_000913 | 4,219,372 | 0 | T | C | 46.4% | 34.5 / 200.9 | 140 | V259V (GTT→GTC) | aceK | isocitrate dehydrogenase kinase/phosphatase |
| * | NC_000913 | 4,614,395 | 0 | T | C | 44.6% | 98.9 / 152.0 | 112 | intergenic (+135/+285) | yjjV/yjjW | putative metal‑dependent hydrolase YjjV/putative glycyl‑radical enzyme activating enzyme YjjW |
| * | NC_000913 | 1,720,453 | 0 | C | T | 44.3% | 33.4 / 121.5 | 88 | E124E (GAG→GAA) | slyA | DNA‑binding transcriptional dual regulator SlyA |
| * | NC_000913 | 3,728,118 | 1 | . | C | 42.9% | 16.6 / 95.3 | 56 | coding (1254/1455 nt) | xylB | xylulokinase |
| * | NC_000913 | 3,728,118 | 0 | C | . | 39.3% | 113.9 / 78.5 | 56 | coding (1254/1455 nt) | xylB | xylulokinase |
| * | NC_000913 | 4,614,402 | 0 | C | T | 37.2% | 131.7 / 110.9 | 102 | intergenic (+142/+278) | yjjV/yjjW | putative metal‑dependent hydrolase YjjV/putative glycyl‑radical enzyme activating enzyme YjjW |
| * | NC_000913 | 1,621,118 | 0 | A | C | 36.2% | 124.5 / 22.0 | 80 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| * | NC_000913 | 3,003,921 | 0 | T | G | 35.6% | 173.4 / 17.6 | 90 | Y145D (TAT→GAT) | xdhC | putative xanthine dehydrogenase iron‑sulfur‑binding subunit XdhC |
| * | NC_000913 | 989,943 | 0 | T | G | 34.8% | 193.9 / 13.0 | 143 | S138S (TCA→TCC) | pncB | nicotinate phosphoribosyltransferase |
| * | NC_000913 | 2,483,254 | 0 | G | A | 34.5% | 93.6 / 18.1 | 55 | S29L (TCA→TTA) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| * | NC_000913 | 4,429,984 | 0 | T | G | 32.6% | 188.3 / 21.0 | 97 | L41V (TTG→GTG) | cycA | D‑serine/alanine/glycine/:H(+)symporter |
| * | NC_000913 | 4,213,778 | 0 | A | C | 32.6% | 260.6 / 29.3 | 138 | F116V (TTC→GTC) | yjaB | peptidyl‑lysine N‑acetyltransferase YjaB |
| * | NC_000913 | 4,296,268 | 0 | T | C | 32.0% | 107.9 / 68.5 | 76 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,911 | 0 | G | A | 31.9% | 68.3 / 20.9 | 47 | intergenic (‑122/+1) | fliA/fliX | RNA polymerase sigma factor FliA/small RNA FliX |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.9% | 83.0 / 10.3 | 47 | noncoding (189/195 nt) | fliX | small RNA FliX |
| * | NC_000913 | 4,161,142 | 0 | C | A | 31.4% | 213.9 / 44.2 | 118 | Q26K (CAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 1,292,458 | 0 | T | A | 31.3% | 126.2 / 27.6 | 67 | intergenic (+93/+51) | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase/DNA‑binding transcriptional dual regulator H‑NS |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 20 (0.140) | 32 (0.230) | 30/452 | 3.1 | 49.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 46 (0.340) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4507459 = | NA (NA) | 27 (0.190) | 26/466 | 3.5 | 19.7% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4640419 | 110 (0.780) | coding (18/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | = 257907 | 2 (0.010) | 26 (0.190) | 25/454 | 3.6 | 96.4% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 1034135 | 136 (0.950) | 22 (0.150) | 22/470 | 4.0 | 13.9% | coding (882/1794 nt) | hyaB | hydrogenase 1 large subunit |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 280111 | NA (NA) | 23 (0.160) | 22/466 | 4.0 | 17.3% | noncoding (181/181 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4640419 | 110 (0.780) | coding (18/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 23 (0.160) | 22/464 | 4.0 | 17.4% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4640419 | 110 (0.780) | coding (18/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | = 1395078 | 90 (0.630) | 20 (0.140) | 20/470 | 4.3 | 18.2% | coding (845/1032 nt) | ynaI | small conductance mechanosensitive channel YnaI |
| ? | NC_000913 | 1396044 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1034134 = | 130 (0.920) | 16 (0.110) | 16/466 | 4.8 | 11.0% | coding (881/1794 nt) | hyaB | hydrogenase 1 large subunit |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 280111 | NA (NA) | 16 (0.110) | 16/470 | 4.8 | 10.5% | noncoding (181/181 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1034135 | 136 (0.950) | coding (882/1794 nt) | hyaB | hydrogenase 1 large subunit | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 16 (0.110) | 16/468 | 4.8 | 10.6% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1034135 | 136 (0.950) | coding (882/1794 nt) | hyaB | hydrogenase 1 large subunit | |||||