mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 1,666,466 | 0 | T→G | 18.8% | 13.8 ‑1.0 ‑0.5 | 32 | Y384* (TAT→TAG) | clcB | H(+)/Cl(‑) exchange transporter |
| * | NC_000913 | 1,666,470 | 0 | C→A | 20.0% | 13.3 ‑1.0 ‑0.1 | 30 | L386I (CTA→ATA) | clcB | H(+)/Cl(‑) exchange transporter |
| * | NC_000913 | 3,250,989 | 0 | G→C | 10.3% | 12.6 ‑1.0 ‑0.3 | 58 | intergenic (+35/‑35) | yqjF/yqjG | putative quinol oxidase subunit/putative S‑transferase |
| * | NC_000913 | 1,666,468 | 0 | A→T | 19.4% | 11.7 ‑1.0 ‑0.3 | 31 | Q385L (CAG→CTG) | clcB | H(+)/Cl(‑) exchange transporter |
| * | NC_000913 | 1,571,595 | 0 | G→T | 100.0% | 0.9 | 1 | P151T (CCA→ACA) | gadB | glutamate decarboxylase B, PLP‑dependent |
| * | NC_000913 | 1,433,862 | 0 | C→A | 100.0% | 0.8 | 1 | intergenic (‑188/+129) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| * | NC_000913 | 566,953 | 0 | G→C | 100.0% | 0.7 | 1 | E38Q (GAA→CAA) | insE1 | IS3 transposase A |
| * | NC_000913 | 4,035,937 | 0 | T→G | 100.0% | 0.6 | 1 | noncoding (407/1542 nt) | rrsA | 16S ribosomal RNA of rrnA operon |
| * | NC_000913 | 3,622,094 | 0 | A→C | 100.0% | 0.5 | 1 | H968P (CAT→CCT) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,619,466 | 0 | T→C | 100.0% | 0.4 | 1 | L92P (CTC→CCC) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,943,768 | 0 | T→C | 100.0% | 0.4 | 1 | noncoding (65/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913 | 3,763,879 | 0 | A→G | 100.0% | 0.0 | 2 | E566G (GAG→GGG) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,763,882 | 0 | A→G | 100.0% | 0.0 | 2 | E567G (GAA→GGA) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| * | NC_000913 | 4,038,030 | 0 | G→T | 100.0% | ‑0.0 | 1 | noncoding (512/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 458,738 | 0 | G→A | 19.4% | 11.0 ‑0.9 ‑0.1 | 36 | intergenic (+38/‑150) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| * | NC_000913 | 458,742 | 0 | T→A | 19.4% | 13.7 ‑0.9 ‑0.1 | 37 | intergenic (+42/‑146) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| * | NC_000913 | 458,743 | 0 | T→A | 19.4% | 13.3 ‑0.9 ‑0.0 | 37 | intergenic (+43/‑145) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| * | NC_000913 | 458,744 | 0 | T→A | 18.9% | 10.8 ‑0.9 0.0 | 37 | intergenic (+44/‑144) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| * | NC_000913 | 458,748 | 0 | T→C | 18.4% | 11.4 ‑0.9 ‑0.2 | 38 | intergenic (+48/‑140) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| * | NC_000913 | 1,594,124 | 1 | .→C | 12.9% | 13.9 0.0 ‑0.3 | 31 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| * | NC_000913 | 2,663,466 | 0 | G→T | 11.8% | 11.5 ‑0.4 ‑0.0 | 68 | V9L (GTG→TTG) | suhB | inositol monophosphatase |
| * | NC_000913 | 2,663,474 | 0 | A→T | 10.4% | 11.3 0.0 ‑0.1 | 67 | A11A (GCA→GCT) | suhB | inositol monophosphatase |
| * | NC_000913 | 2,663,482 | 0 | A→C | 10.1% | 13.8 0.0 ‑0.1 | 70 | K14T (AAG→ACG) | suhB | inositol monophosphatase |
| * | NC_000913 | 2,673,784 | 0 | C→A | 10.0% | 11.6 ‑0.4 ‑0.2 | 61 | intergenic (+16/+32) | yphA/yphB | DoxX family inner membrane protein/mutarotase superfamily protein, YphB family |
| * | NC_000913 | 2,673,790 | 0 | G→T | 12.5% | 12.1 ‑0.3 ‑0.0 | 64 | intergenic (+22/+26) | yphA/yphB | DoxX family inner membrane protein/mutarotase superfamily protein, YphB family |
| * | NC_000913 | 2,673,791 | 0 | A→C | 10.9% | 12.8 0.0 ‑0.1 | 64 | intergenic (+23/+25) | yphA/yphB | DoxX family inner membrane protein/mutarotase superfamily protein, YphB family |
| * | NC_000913 | 3,946,620 | 0 | A→C | 25.4% | 40.0 ‑0.3 ‑0.1 | 59 | intergenic (+13/‑80) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| * | NC_000913 | 4,060,261 | 0 | G→T | 17.5% | 12.8 ‑0.9 ‑0.0 | 40 | intergenic (+31/‑186) | typA/yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 4,060,264 | 0 | A→C | 15.0% | 13.6 ‑0.4 ‑0.6 | 40 | intergenic (+34/‑183) | typA/yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 4,296,060 | 0 | C→T | 23.3% | 12.4 0.0 ‑0.0 | 33 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 2611254 = | 43 (1.140) | 4 (0.110) | 4/404 | 4.6 | 7.7% | coding (549/759 nt) | hyfI | hydrogenase 4, Fe‑S subunit |
| ? | NC_000913 | 2611305 = | 55 (1.510) | coding (600/759 nt) | hyfI | hydrogenase 4, Fe‑S subunit | |||||
| * | ? | NC_000913 | 351579 = | 29 (0.770) | 3 (0.080) | 3/402 | 5.1 | 10.2% | coding (365/1452 nt) | prpD | 2‑methylcitrate dehydratase |
| ? | NC_000913 | 351632 = | 25 (0.690) | coding (418/1452 nt) | prpD | 2‑methylcitrate dehydratase | |||||
| * | ? | NC_000913 | 424447 = | 40 (1.060) | 3 (0.080) | 3/402 | 5.1 | 7.8% | coding (472/582 nt) | acpH | acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase |
| ? | NC_000913 | 424497 = | 32 (0.890) | coding (422/582 nt) | acpH | acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase | |||||
| * | ? | NC_000913 | 643269 = | 28 (0.740) | 3 (0.080) | 3/404 | 5.1 | 11.5% | coding (1182/1239 nt) | ybdR | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| ? | NC_000913 | 643379 = | 19 (0.520) | intergenic (+53/+178) | ybdR/rnk | putative Zn‑dependent NAD(P)‑binding oxidoreductase/regulator of nucleoside diphosphate kinase | |||||
| * | ? | NC_000913 | 1859579 = | 20 (0.530) | 3 (0.080) | 3/404 | 5.1 | 11.9% | coding (651/1380 nt) | ydjK | putative MFS sugar transporter, membrane protein |
| ? | NC_000913 | 1859626 = | 25 (0.690) | coding (604/1380 nt) | ydjK | putative MFS sugar transporter, membrane protein | |||||
| * | ? | NC_000913 | 2243148 = | 37 (0.980) | 3 (0.080) | 3/402 | 5.1 | 8.2% | coding (505/669 nt) | folE | GTP cyclohydrolase I |
| ? | NC_000913 | 2243219 = | 32 (0.890) | coding (434/669 nt) | folE | GTP cyclohydrolase I | |||||
| * | ? | NC_000913 | 3247830 = | 62 (1.650) | 3 (0.080) | 3/404 | 5.1 | 4.7% | coding (58/663 nt) | yqjA | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| ? | NC_000913 | 3247851 = | 62 (1.710) | coding (79/663 nt) | yqjA | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter | |||||
| * | ? | NC_000913 | 3390623 = | 26 (0.690) | 3 (0.080) | 3/406 | 5.2 | 10.1% | coding (1406/1446 nt) | tldD | putative peptidase |
| ? | NC_000913 | 3390643 = | 28 (0.770) | coding (1386/1446 nt) | tldD | putative peptidase | |||||
| * | ? | NC_000913 | = 3872858 | 31 (0.820) | 4 (0.110) | 3/412 | 5.2 | 11.7% | coding (141/1149 nt) | dgoD | D‑galactonate dehydratase |
| ? | NC_000913 | = 3872904 | 30 (0.810) | coding (95/1149 nt) | dgoD | D‑galactonate dehydratase | |||||