mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,365,541 | 0 | A | G | 51.8% | 13.8 / 200.0 | 141 | pseudogene (357/371 nt) | yhcE | putative uncharacterized protein YhcE |
| * | NC_000913 | 109,908 | 0 | C | T | 50.0% | ‑6.1 / 38.2 | 30 | R544C (CGT→TGT) | secA | protein translocation ATPase |
| * | NC_000913 | 2,734,536 | 0 | C | . | 50.0% | 68.4 / 83.2 | 44 | coding (499/732 nt) | pgeF | polyphenol oxidase YfiH |
| * | NC_000913 | 4,606,086 | 1 | . | G | 50.0% | 42.5 / 55.1 | 30 | noncoding (80/87 nt) | leuV | tRNA‑Leu |
| * | NC_000913 | 340,071 | 0 | A | G | 49.2% | ‑3.0 / 87.2 | 61 | R93R (CGA→CGG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 4,604,344 | 0 | C | T | 44.2% | 45.2 / 34.6 | 52 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,606,095 | 0 | A | G | 40.6% | 12.3 / 31.1 | 35 | noncoding (71/87 nt) | leuV | tRNA‑Leu |
| * | NC_000913 | 2,591,604 | 0 | T | C | 40.0% | 32.3 / 58.8 | 55 | intergenic (+1/‑3) | yffB/dapE | putative reductase YffB/succinyl‑diaminopimelate desuccinylase |
| * | NC_000913 | 924,225 | 0 | C | T | 37.2% | 41.0 / 49.8 | 51 | S321L (TCG→TTG) | clpA | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| * | NC_000913 | 4,074,912 | 1 | . | A | 37.2% | 15.7 / 76.8 | 43 | coding (244/786 nt) | yihW | putative DNA‑binding transcriptional regulator YihW |
| * | NC_000913 | 340,085 | 1 | . | T | 37.0% | 19.1 / 81.1 | 46 | coding (293/297 nt) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 3,017,169 | 0 | G | A | 35.9% | 59.2 / 62.0 | 65 | L370L (CTG→CTA) | ygfK | putative oxidoreductase, Fe‑S subunit |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.5% | 44.9 / 12.2 | 31 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,068,173 | 0 | T | G | 33.3% | 58.3 / 11.0 | 37 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,315,519 | 0 | T | C | 33.3% | 52.7 / 44.0 | 51 | E84E (GAA→GAG) | yciF | DUF892 domain‑containing protein YciF |
| * | NC_000913 | 3,525,418 | 0 | T | C | 31.4% | 41.7 / 23.7 | 35 | F850L (TTC→CTC) | mrcA | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| * | NC_000913 | 373,920 | 0 | A | G | 31.1% | 54.7 / 33.2 | 45 | H18R (CAC→CGC) | mhpE | 4‑hydroxy‑2‑oxovalerate aldolase |
| * | NC_000913 | 29,496 | 0 | T | A | 27.6% | 61.5 / 10.4 | 29 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.0% | 79.6 / 30.3 | 51 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.0% | 106.6 / 12.3 | 50 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 2518092 = | 51 (1.010) | 8 (0.180) | 8/240 | 3.0 | 15.3% | noncoding (25/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2521076 = | 44 (1.000) | noncoding (26/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | 2514273 = | NA (NA) | 8 (0.200) | 7/224 | 3.0 | 20.0% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2515618 = | 32 (0.780) | intergenic (+175/+25) | insL‑3/pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA | |||||
| * | ? | NC_000913 | = 555833 | 48 (0.950) | 11 (0.250) | 8/244 | 3.0 | 21.9% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 36 (0.810) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | = 339821 | NA (NA) | 14 (0.310) | 8/248 | 3.1 | NA | noncoding (17/29 nt) | other | REPv23b |
| ? | NC_000913 | = 377457 | NA (NA) | noncoding (22/37 nt) | other | REP32c | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 18 (0.380) | 8/260 | 3.2 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374945 = | NA (NA) | 9 (0.180) +T |
8/274 | 3.4 | NA | noncoding (15/34 nt) | other | REP31a |
| ? | NC_000913 | 377408 = | NA (NA) | noncoding (15/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | = 2288554 | 0 (0.000) | 7 (0.140) +CCCC |
6/254 | 3.7 | 100% | pseudogene (361/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| ? | NC_000913 | 2288555 = | 0 (0.000) | pseudogene (360/2525 nt) | yejO | adhesin‑like autotransporter YejO | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 6 (0.120) +T |
6/274 | 4.0 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 159901 | 61 (1.210) | 5 (0.110) | 5/252 | 4.1 | 8.4% | coding (212/927 nt) | gluQ | glutamyl‑Q tRNA(Asp) synthetase |
| ? | NC_000913 | = 160488 | 53 (1.150) | coding (117/456 nt) | dksA | RNA polymerase‑binding transcription factor DksA | |||||
| * | ? | NC_000913 | 2827789 = | 30 (0.590) | 5 (0.110) | 5/260 | 4.2 | 13.5% | coding (53/780 nt) | srlD | sorbitol‑6‑phosphate 2‑dehydrogenase |
| ? | NC_000913 | 2827868 = | 36 (0.760) | coding (132/780 nt) | srlD | sorbitol‑6‑phosphate 2‑dehydrogenase | |||||