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 | 4,296,060 | 0 | C→T | 19.7% | 29.7 ‑3.4 ‑0.0 | 71 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 380,012 | 1 | .→G | 13.5% | 19.8 ‑3.2 ‑0.3 | 37 | intergenic (‑131/+57) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| * | NC_000913 | 3,781,120 | 0 | T→C | 28.6% | 15.0 ‑7.5 0.0 | 36 | intergenic (+103/‑95) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,781,140 | 0 | A→G | 38.7% | 12.9 ‑5.7 0.0 | 31 | intergenic (+123/‑75) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,781,152 | 0 | A→G | 30.3% | 12.5 ‑5.0 ‑0.0 | 33 | intergenic (+135/‑63) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,424,856 | 0 | T→G | 100.0% | 1.0 | 1 | noncoding (1928/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,915,645 | 0 | G→T | 100.0% | 0.7 | 1 | H110N (CAC→AAC) | atpC | F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| * | NC_000913 | 3,915,920 | 0 | G→T | 100.0% | 0.7 | 1 | S18Y (TCT→TAT) | atpC | F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| * | NC_000913 | 3,366,553 | 0 | A→C | 100.0% | 0.6 | 1 | F56V (TTT→GTT) | insH1 | IS5 transposase and trans‑activator |
| * | NC_000913 | 3,915,743 | 0 | A→G | 100.0% | 0.6 | 1 | V77A (GTG→GCG) | atpC | F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| * | NC_000913 | 279,743 | 0 | A→G | 100.0% | 0.5 | 1 | Y45H (TAC→CAC) | insA | IS1 repressor TnpA |
| * | NC_000913 | 270,735 | 0 | G→C | 100.0% | 0.4 | 1 | G45R (GGC→CGC) | insI1 | IS30 transposase |
| * | NC_000913 | 270,738 | 0 | G→C | 100.0% | 0.4 | 1 | G46R (GGC→CGC) | insI1 | IS30 transposase |
| * | NC_000913 | 3,470,369 | 0 | T→A | 100.0% | 0.0 | 1 | T321S (ACT→TCT) | tufA | translation elongation factor EF‑Tu 1 |
| * | NC_000913 | 3,427,148 | 0 | A→G | 100.0% | ‑0.2 | 1 | noncoding (5/77 nt) | ileU | tRNA‑Ile |
| * | NC_000913 | 3,427,164 | 0 | A→C | 100.0% | ‑0.2 | 1 | intergenic (‑12/+57) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,171 | 0 | A→T | 100.0% | ‑0.2 | 1 | intergenic (‑19/+50) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,175 | 0 | T→A | 100.0% | ‑0.2 | 1 | intergenic (‑23/+46) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,179 | 0 | C→A | 100.0% | ‑0.2 | 1 | intergenic (‑27/+42) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,183 | 0 | C→A | 100.0% | ‑0.2 | 1 | intergenic (‑31/+38) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,186 | 0 | T→C | 100.0% | ‑0.2 | 1 | intergenic (‑34/+35) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,427,187 | 0 | C→T | 100.0% | ‑0.2 | 1 | intergenic (‑35/+34) | ileU/rrsD | tRNA‑Ile/16S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,424,984 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (1800/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,424,985 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (1799/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,424,987 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (1797/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,424,989 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (1795/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 556,640 | 0 | T→A | 11.7% | 12.6 ‑0.4 ‑0.5 | 60 | intergenic (‑87/+21) | ybcI/ybcJ | DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein |
| * | NC_000913 | 556,641 | 0 | G→T | 13.6% | 12.6 0.0 0.0 | 59 | intergenic (‑88/+20) | ybcI/ybcJ | DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein |
| * | NC_000913 | 556,642 | 0 | A→C | 13.8% | 16.2 0.0 ‑0.0 | 59 | intergenic (‑89/+19) | ybcI/ybcJ | DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein |
| * | NC_000913 | 556,643 | 0 | T→A | 12.5% | 12.8 ‑0.4 ‑0.2 | 58 | intergenic (‑90/+18) | ybcI/ybcJ | DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein |
| * | NC_000913 | 1,297,267 | 0 | A→G | 12.7% | 12.6 ‑0.4 ‑0.5 | 55 | V285V (GTT→GTC) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| * | NC_000913 | 1,297,268 | 0 | A→T | 12.7% | 13.2 ‑0.4 ‑0.5 | 55 | V285D (GTT→GAT) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| * | NC_000913 | 1,297,269 | 0 | C→T | 13.0% | 12.3 ‑0.4 ‑0.4 | 54 | V285I (GTT→ATT) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| * | NC_000913 | 3,181,600 | 0 | A→G | 11.5% | 11.6 0.0 ‑0.1 | 62 | intergenic (+19/+19) | ygiC/ygiD | ATP‑Grasp family ATPase/4,5‑ DOPA‑extradiol‑dioxygenase |
| * | NC_000913 | 3,181,601 | 0 | C→A | 11.3% | 13.8 0.0 ‑0.2 | 62 | intergenic (+20/+18) | ygiC/ygiD | ATP‑Grasp family ATPase/4,5‑ DOPA‑extradiol‑dioxygenase |
| * | NC_000913 | 3,181,602 | 0 | T→G | 11.5% | 15.1 0.0 ‑0.3 | 61 | intergenic (+21/+17) | ygiC/ygiD | ATP‑Grasp family ATPase/4,5‑ DOPA‑extradiol‑dioxygenase |
| * | NC_000913 | 3,181,603 | 0 | C→T | 11.7% | 11.5 0.0 ‑0.3 | 61 | intergenic (+22/+16) | ygiC/ygiD | ATP‑Grasp family ATPase/4,5‑ DOPA‑extradiol‑dioxygenase |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315651 | NA (NA) | 6 (0.120) | 5/402 | 7.7 | NA | noncoding (423/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315703 | NA (NA) | noncoding (475/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 42 (0.780) | 5 (0.100) | 5/386 | 7.5 | 11.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 35 (0.710) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2705894 | 63 (1.180) | 4 (0.080) | 4/400 | 8.3 | 6.3% | coding (1231/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase |
| ? | NC_000913 | = 2705947 | 58 (1.130) | coding (1178/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase | |||||
| * | ? | NC_000913 | = 3414185 | 63 (1.180) | 4 (0.080) | 4/406 | 8.4 | 6.1% | coding (322/1158 nt) | acrE | cytoplasmic membrane lipoprotein |
| ? | NC_000913 | = 3414221 | 62 (1.190) | coding (358/1158 nt) | acrE | cytoplasmic membrane lipoprotein | |||||
| * | ? | NC_000913 | 224575 = | 1 (0.020) | 3 (0.060) | 3/404 | 9.1 | 75.6% | noncoding (805/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 2730305 | NA (NA) | noncoding (853/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 2006460 | 45 (0.840) | 3 (0.060) | 3/406 | 9.1 | 6.3% | coding (305/1488 nt) | amyA | cytoplasmic alpha‑amylase |
| ? | NC_000913 | = 2006465 | 45 (0.860) | coding (310/1488 nt) | amyA | cytoplasmic alpha‑amylase | |||||
| * | ? | NC_000913 | 2647212 = | 62 (1.160) | 3 (0.060) | 3/412 | 9.2 | 4.8% | coding (114/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| ? | NC_000913 | 2647262 = | 57 (1.080) | coding (64/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein | |||||
| * | ? | NC_000913 | = 2730312 | NA (NA) | 3 (0.060) | 3/404 | 9.1 | NA | noncoding (846/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730346 | NA (NA) | noncoding (812/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | 4080093 = | 52 (0.970) | 3 (0.060) | 3/404 | 9.1 | 5.6% | noncoding (74/98 nt) | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 4080118 = | 51 (0.990) | intergenic (+149/+181) | yiiF/fdhE | putative thymol sensitivity protein, CopG family putative transcriptional regulator/formate dehydrogenase formation protein | |||||
| * | ? | NC_000913 | 4142066 = | 46 (0.860) | 3 (0.060) | 3/400 | 9.0 | 6.2% | coding (156/2502 nt) | frwA | putative PTS enzyme: Hpr, enzyme I and II components |
| ? | NC_000913 | 4142096 = | 47 (0.920) | coding (126/2502 nt) | frwA | putative PTS enzyme: Hpr, enzyme I and II components | |||||