mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.0% | 47.2 / 44.9 | 46 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 857,576 | 0 | T | C | 30.0% | 25.3 / 11.8 | 20 | intergenic (+21/+220) | ybiT/ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| * | NC_000913 | 2,536,370 | 0 | C | G | 30.0% | 21.3 / 15.0 | 20 | intergenic (+27/+16) | crr/pdxK | glucose‑specific enzyme IIA component of PTS/pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| * | NC_000913 | 2,536,373 | 0 | C | G | 30.0% | 30.4 / 11.9 | 20 | intergenic (+30/+13) | crr/pdxK | glucose‑specific enzyme IIA component of PTS/pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| * | NC_000913 | 987,418 | 0 | A | T | 28.6% | 28.8 / 12.6 | 21 | intergenic (‑436/+167) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 857,578 | 0 | C | G | 27.3% | 39.2 / 15.0 | 22 | intergenic (+23/+218) | ybiT/ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| * | NC_000913 | 857,580 | 0 | G | A | 25.0% | 40.5 / 11.5 | 24 | intergenic (+25/+216) | ybiT/ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| * | NC_000913 | 691,390 | 0 | G | C | 23.3% | 57.6 / 16.2 | 30 | A132G (GCC→GGC) | ybeX | putative ion transport |
| * | NC_000913 | 987,420 | 0 | A | C | 23.1% | 46.8 / 12.4 | 26 | intergenic (‑438/+165) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 987,421 | 0 | A | T | 23.1% | 48.6 / 11.9 | 26 | intergenic (‑439/+164) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 987,422 | 0 | G | T | 22.2% | 57.9 / 12.3 | 27 | intergenic (‑440/+163) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 987,424 | 0 | A | T | 22.2% | 53.9 / 10.2 | 27 | intergenic (‑442/+161) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 1,576,374 | 0 | T | C | 21.4% | 52.6 / 10.4 | 28 | T416A (ACT→GCT) | yddB | putative TonB‑dependent outer membrane receptor |
| * | NC_000913 | 1,865,682 | 0 | G | C | 20.0% | 88.6 / 19.8 | 40 | intergenic (‑46/+44) | yeaE/mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| * | NC_000913 | 3,052,890 | 0 | A | C | 20.0% | 68.3 / 16.5 | 35 | L210R (CTG→CGG) | ubiH | 2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding |
| * | NC_000913 | 4,520,500 | 0 | A | . | 20.0% | 140.6 / 30.7 | 50 | intergenic (‑176/+171) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Marginal new junction evidence (lowest skew 10 of 65 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1411899 = | 52 (1.410) | 7 (0.240) | 7/204 | 2.7 | 19.1% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 18 (0.610) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2253491 = | 40 (1.080) | 7 (0.200) | 7/244 | 3.3 | 15.0% | coding (655/1251 nt) | nupX | nucleoside permease |
| ? | NC_000913 | 2253513 = | 41 (1.160) | coding (633/1251 nt) | nupX | nucleoside permease | |||||
| * | ? | NC_000913 | 2514274 = | NA (NA) | 7 (0.190) | 7/252 | 3.4 | 31.8% | noncoding (2/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2536312 = | 15 (0.410) | coding (479/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | 377335 = | NA (NA) | 6 (0.200) +25 bp |
5/206 | 3.4 | NA | noncoding (1/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913 | 3139626 = | NA (NA) | noncoding (6/83 nt) | REP221 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP221 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2267505 = | 19 (0.510) | 6 (0.170) | 6/240 | 3.5 | 24.1% | coding (1261/1467 nt) | yeiQ | putative NAD‑dependent D‑mannonate oxidoreductase |
| ? | NC_000913 | 2267539 = | 20 (0.580) | coding (1295/1467 nt) | yeiQ | putative NAD‑dependent D‑mannonate oxidoreductase | |||||
| * | ? | NC_000913 | = 1522204 | 33 (0.890) | 6 (0.180) | 6/236 | 3.5 | 16.1% | coding (862/2103 nt) | yncD | putative iron outer membrane transporter |
| ? | NC_000913 | = 1522222 | 32 (0.940) | coding (844/2103 nt) | yncD | putative iron outer membrane transporter | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 7 (0.200) | 6/238 | 3.5 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4584195 = | 36 (0.970) | 6 (0.170) | 6/242 | 3.6 | 15.4% | coding (2567/3513 nt) | hsdR | endonuclease R Type I restriction enzyme |
| ? | NC_000913 | 4584232 = | 32 (0.920) | coding (2530/3513 nt) | hsdR | endonuclease R Type I restriction enzyme | |||||
| * | ? | NC_000913 | = 1333679 | 46 (1.240) | 6 (0.170) | 6/244 | 3.6 | 11.9% | intergenic (+34/‑176) | topA/cysB | DNA topoisomerase I, omega subunit/N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor |
| ? | NC_000913 | = 1333691 | 45 (1.280) | intergenic (+46/‑164) | topA/cysB | DNA topoisomerase I, omega subunit/N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor | |||||
| * | ? | NC_000913 | = 258309 | NA (NA) | 7 (0.200) | 6/244 | 3.6 | NA | noncoding (367/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 279590 | NA (NA) | noncoding (341/768 nt) | IS1 | repeat region | |||||