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 | 3,781,145 | 0 | C→G | 17.8% | 10.0 ‑8.5 ‑0.0 | 45 | intergenic (+128/‑70) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 526,073 | 0 | A→C | 100.0% | 1.3 | 1 | N938T (AAC→ACC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,943,212 | 0 | G→T | 100.0% | 0.8 | 1 | noncoding (1405/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| * | NC_000913 | 1,633,425 | 0 | G→T | 100.0% | 0.7 | 1 | intergenic (+120/‑197) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 3,666,682 | 0 | A→C | 100.0% | 0.7 | 1 | V300G (GTG→GGG) | gadA | glutamate decarboxylase A, PLP‑dependent |
| * | NC_000913 | 3,943,209 | 0 | C→G | 100.0% | 0.7 | 1 | noncoding (1402/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| * | NC_000913 | 3,943,216 | 0 | C→A | 100.0% | 0.7 | 1 | noncoding (1409/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| * | NC_000913 | 1,300,652 | 0 | T→G | 100.0% | 0.6 | 1 | intergenic (+1407/‑530) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,666,601 | 0 | T→G | 100.0% | 0.5 | 1 | Q327P (CAG→CCG) | gadA | glutamate decarboxylase A, PLP‑dependent |
| * | NC_000913 | 526,071 | 0 | T→C | 100.0% | 0.4 | 1 | D937D (GAT→GAC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,944,264 | 0 | G→A | 100.0% | 0.3 | 2 | noncoding (561/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913 | 3,622,097 | 0 | A→C | 100.0% | 0.1 | 2 | Y969S (TAC→TCC) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 4,508,363 | 0 | A→C | 100.0% | ‑0.1 | 1 | N85K (AAT→AAG) | insI1 | IS30 transposase |
| * | NC_000913 | 4,508,365 | 0 | T→G | 100.0% | ‑0.1 | 1 | N85H (AAT→CAT) | insI1 | IS30 transposase |
| * | NC_000913 | 4,508,366 | 0 | C→A | 100.0% | ‑0.1 | 1 | L84L (CTG→CTT) | insI1 | IS30 transposase |
| * | NC_000913 | 4,508,368 | 0 | G→T | 100.0% | ‑0.1 | 1 | L84M (CTG→ATG) | insI1 | IS30 transposase |
| * | NC_000913 | 4,508,189 | 0 | C→T | 100.0% | ‑0.2 | 1 | W143* (TGG→TGA) | insI1 | IS30 transposase |
| * | NC_000913 | 4,508,204 | 0 | C→G | 100.0% | ‑0.2 | 1 | K138N (AAG→AAC) | insI1 | IS30 transposase |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 1,743,155 | 0 | C→G | 12.9% | 21.0 ‑0.7 ‑0.1 | 70 | D30H (GAC→CAC) | ribC | riboflavin synthase, alpha subunit |
| * | NC_000913 | 1,743,157 | 0 | G→A | 12.9% | 16.9 ‑0.7 ‑0.6 | 70 | P29L (CCC→CTC) | ribC | riboflavin synthase, alpha subunit |
| * | NC_000913 | 1,743,160 | 0 | A→T | 13.0% | 18.4 ‑0.7 ‑0.4 | 69 | L28* (TTA→TAA) | ribC | riboflavin synthase, alpha subunit |
| * | NC_000913 | 1,743,163 | 0 | T→C | 13.0% | 17.7 ‑0.7 ‑0.8 | 69 | E27G (GAG→GGG) | ribC | riboflavin synthase, alpha subunit |
| * | NC_000913 | 1,743,165 | 0 | C→G | 13.4% | 22.7 ‑0.7 ‑0.6 | 67 | V26V (GTG→GTC) | ribC | riboflavin synthase, alpha subunit |
| * | NC_000913 | 3,503,971 | 0 | C→G | 10.9% | 10.0 0.0 ‑0.2 | 55 | intergenic (+19/‑81) | frlD/frlR | fructoselysine 6‑kinase/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 3,503,974 | 0 | C→G | 11.1% | 12.9 0.0 ‑0.7 | 54 | intergenic (+22/‑78) | frlD/frlR | fructoselysine 6‑kinase/putative DNA‑binding transcriptional regulator |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 41 (0.890) | 8 (0.190) | 8/386 | 5.0 | 18.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 35 (0.820) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3603646 = | 42 (0.910) | 5 (0.110) | 5/408 | 6.7 | 9.5% | coding (598/1494 nt) | ftsY | Signal Recognition Particle (SRP) receptor |
| ? | NC_000913 | 3603693 = | 54 (1.200) | coding (551/1494 nt) | ftsY | Signal Recognition Particle (SRP) receptor | |||||
| * | ? | NC_000913 | = 1207805 | 41 (0.890) | 4 (0.090) | 4/386 | 6.9 | 9.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 35 (0.820) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 198033 = | 49 (1.060) | 3 (0.070) | 3/400 | 7.8 | 5.8% | coding (106/2433 nt) | bamA | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| ? | NC_000913 | 198087 = | 51 (1.160) | coding (160/2433 nt) | bamA | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor | |||||
| * | ? | NC_000913 | 797071 = | 35 (0.760) | 3 (0.070) | 3/402 | 7.9 | 7.6% | coding (518/1059 nt) | modC | molybdate ABC transporter ATPase; chlorate resistance protein |
| ? | NC_000913 | 797113 = | 39 (0.880) | coding (560/1059 nt) | modC | molybdate ABC transporter ATPase; chlorate resistance protein | |||||
| * | ? | NC_000913 | = 1324836 | 59 (1.280) | 3 (0.070) | 3/392 | 7.7 | 5.1% | coding (91/1896 nt) | yciQ | enhancer of membrane protein expression; putative inner membrane protein |
| ? | NC_000913 | = 1324839 | 57 (1.320) | coding (94/1896 nt) | yciQ | enhancer of membrane protein expression; putative inner membrane protein | |||||
| * | ? | NC_000913 | 1403894 = | 42 (0.910) | 4 (0.090) | 3/412 | 8.0 | 9.0% | coding (672/1311 nt) | abgA | p‑aminobenzoyl‑glutamate hydrolase, A subunit |
| ? | NC_000913 | 1403942 = | 39 (0.860) | coding (624/1311 nt) | abgA | p‑aminobenzoyl‑glutamate hydrolase, A subunit | |||||
| * | ? | NC_000913 | 1808116 = | 40 (0.870) | 3 (0.070) | 3/402 | 7.9 | 7.7% | coding (321/861 nt) | yniA | fructosamine kinase family protein |
| ? | NC_000913 | 1808242 = | 33 (0.740) | coding (447/861 nt) | yniA | fructosamine kinase family protein | |||||
| * | ? | NC_000913 | 2032675 = | 56 (1.210) | 3 (0.070) | 3/398 | 7.8 | 5.3% | coding (405/696 nt) | yedJ | putative HD superfamily phosphohydrolase |
| ? | NC_000913 | 2032745 = | 54 (1.230) | coding (335/696 nt) | yedJ | putative HD superfamily phosphohydrolase | |||||
| * | ? | NC_000913 | 2426464 = | 38 (0.820) | 3 (0.070) | 3/402 | 7.9 | 6.6% | coding (325/783 nt) | hisJ | histidine ABC transporter periplasmic binding protein |
| ? | NC_000913 | 2426586 = | 48 (1.080) | coding (203/783 nt) | hisJ | histidine ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2553449 = | 47 (1.020) | 3 (0.070) | 3/412 | 8.0 | 6.0% | coding (225/900 nt) | hemF | coproporphyrinogen III oxidase |
| ? | NC_000913 | 2553496 = | 48 (1.060) | coding (272/900 nt) | hemF | coproporphyrinogen III oxidase | |||||
| * | ? | NC_000913 | = 2763709 | 49 (1.060) | 3 (0.070) | 3/412 | 8.0 | 6.2% | coding (1445/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| ? | NC_000913 | = 2763778 | 42 (0.920) | coding (1376/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein | |||||
| * | ? | NC_000913 | 3071408 = | 42 (0.910) | 3 (0.070) | 3/408 | 7.9 | 6.6% | intergenic (‑164/+51) | fbaA/pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| ? | NC_000913 | 3071485 = | 44 (0.980) | coding (1138/1164 nt) | pgk | phosphoglycerate kinase | |||||
| * | ? | NC_000913 | 3378252 = | 61 (1.320) | 3 (0.070) | 3/410 | 8.0 | 5.1% | coding (400/429 nt) | rplM | 50S ribosomal subunit protein L13 |
| ? | NC_000913 | 3378316 = | 51 (1.130) | coding (336/429 nt) | rplM | 50S ribosomal subunit protein L13 | |||||
| * | ? | NC_000913 | 4213168 = | 40 (0.870) | 3 (0.070) | 3/396 | 7.8 | 7.3% | intergenic (+9/‑66) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein |
| ? | NC_000913 | 4213199 = | 38 (0.870) | intergenic (+40/‑35) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||