mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 298 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,165,968 | 0 | C | T | 56.4% | 217.0 / inf | 550 | intergenic (+283/‑117) | ycfP/ndh | putative UPF0227 family esterase/respiratory NADH dehydrogenase 2/cupric reductase |
| * | NC_000913 | 2,704,103 | 0 | G | T | 53.4% | 41.0 / inf | 537 | intergenic (‑40/+232) | rnc/lepB | RNase III/leader peptidase (signal peptidase I) |
| * | NC_000913 | 1,828,659 | 0 | G | A | 52.6% | 35.8 / inf | 484 | T359M (ACG→ATG) | astD | succinylglutamic semialdehyde dehydrogenase |
| * | NC_000913 | 4,530,797 | 0 | C | T | 49.4% | 52.6 / inf | 479 | Q285Q (CAG→CAA) | sgcX | putative endoglucanase with Zn‑dependent exopeptidase domain |
| * | NC_000913 | 4,571,280 | 0 | C | T | 48.5% | 101.6 / inf | 497 | E99K (GAG→AAG) | yjiR | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| * | NC_000913 | 3,256,157 | 0 | C | T | 48.4% | 109.8 / inf | 487 | Q165Q (CAG→CAA) | yhaM | putative L‑serine dehydratase alpha chain |
| * | NC_000913 | 4,337,864 | 0 | C | T | 48.3% | 129.3 / inf | 578 | V22V (GTG→GTA) | adiY | adi system transcriptional activator |
| * | NC_000913 | 312,865 | 0 | G | A | 48.2% | 109.4 / inf | 531 | intergenic (‑88/+276) | ykgM/ykgR | 50S ribosomal protein L31 type B; alternative zinc‑limitation L31 protein/uncharacterized protein |
| * | NC_000913 | 3,588,787 | 0 | G | A | 48.2% | 115.9 / inf | 505 | P132S (CCG→TCG) | ugpC | sn‑glycerol‑3‑phosphate ABC transporter ATPase |
| * | NC_000913 | 466,148 | 0 | G | A | 47.9% | 126.8 / inf | 510 | P389S (CCA→TCA) | ybaE | putative ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,046,506 | 0 | G | T | 47.8% | 159.4 / inf | 461 | V523V (GTG→GTT) | yeeJ | putative adhesin |
| * | NC_000913 | 4,435,750 | 0 | C | T | 47.8% | 110.2 / inf | 452 | G272G (GGG→GGA) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase |
| * | NC_000913 | 1,322,759 | 0 | G | A | 47.8% | 120.2 / inf | 450 | A63V (GCT→GTT) | trpE | component I of anthranilate synthase |
| * | NC_000913 | 4,359,909 | 0 | C | T | 47.7% | 101.2 / inf | 528 | W41* (TGG→TGA) | cadB | putative lysine/cadaverine transporter |
| * | NC_000913 | 3,259,283 | 0 | G | A | 47.7% | 119.8 / inf | 524 | H123Y (CAT→TAT) | tdcG | L‑serine dehydratase 3, anaerobic |
| * | NC_000913 | 3,559,621 | 0 | C | T | 47.4% | 110.5 / inf | 434 | P452S (CCC→TCC) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| * | NC_000913 | 2,085,319 | 0 | G | A | 47.4% | 106.1 / inf | 448 | A69A (GCC→GCT) | yeeE | UPF0394 family inner membrane protein |
| * | NC_000913 | 4,553,671 | 0 | C | T | 47.4% | 137.0 / inf | 464 | F257F (TTC→TTT) | uxuB | D‑mannonate oxidoreductase, NAD‑dependent |
| * | NC_000913 | 469,271 | 0 | G | A | 47.3% | 126.3 / inf | 473 | G134E (GGG→GAG) | mdlA | putative multidrug ABC transporter ATPase |
| * | NC_000913 | 4,234,479 | 0 | C | T | 47.3% | 137.2 / inf | 496 | A241V (GCG→GTG) | pgi | glucosephosphate isomerase |
| Marginal new junction evidence (lowest skew 10 of 104 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 275 (0.540) | 170/300 | 3.3 | NA | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4434636 | NA (NA) | coding (1930/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | = 1095502 | NA (NA) | 268 (0.530) | 164/298 | 3.9 | 44.4% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 1199871 | 335 (0.660) | coding (936/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 255 (0.510) | 162/296 | 4.0 | NA | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4434636 | NA (NA) | coding (1930/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | 315229 = | NA (NA) | 274 (0.550) +TC |
162/296 | 4.0 | 44.7% | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 1199872 | 343 (0.670) | coding (935/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 355 (0.700) | 164/300 | 4.0 | 51.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 565828 | 336 (0.660) | coding (151/1164 nt) | intD | DLP12 prophage; putative phage integrase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 256 (0.500) | 161/300 | 4.4 | 41.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 295082 = | 355 (0.700) | intergenic (‑283/+57) | yagM/yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | = 4020781 | 258 (0.510) | 240 (0.470) | 160/300 | 4.5 | 48.1% | coding (556/1641 nt) | ubiB | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase |
| ? | NC_000913 | 4020794 = | 260 (0.510) | coding (569/1641 nt) | ubiB | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase | |||||
| * | ? | NC_000913 | 1909925 = | 321 (0.640) | 388 (0.770) | 159/298 | 4.5 | 54.7% | coding (175/792 nt) | kdgR | KDG regulon transcriptional repressor |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 250 (0.490) | 160/300 | 4.5 | 46.6% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1907403 | 287 (0.560) | coding (33/210 nt) | cspC | stress protein, member of the CspA‑family | |||||
| * | ? | NC_000913 | 1094245 = | NA (NA) | 234 (0.460) | 159/300 | 4.7 | 40.0% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1199869 = | 351 (0.690) | coding (938/1128 nt) | intE | e14 prophage; putative integrase | |||||