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 (highest frequency 20 of 137 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,151,689 | 0 | G | T | 54.5% | ‑3.4 / 19.1 | 34 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 417,533 | 0 | T | G | 50.0% | 26.6 / 39.5 | 86 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 2,151,686 | 0 | G | T | 48.5% | ‑6.2 / 20.7 | 34 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 1,554,000 | 0 | T | G | 38.7% | 178.7 / 16.1 | 111 | Y557S (TAC→TCC) | maeA | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| * | NC_000913 | 2,074,066 | 0 | T | G | 37.5% | 79.0 / 19.8 | 59 | V843G (GTG→GGG) | flu | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| * | NC_000913 | 433,649 | 0 | T | G | 36.0% | 151.0 / 42.5 | 182 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 34.6% | 296.6 / 18.3 | 133 | L41V (TTG→GTG) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | NC_000913 | 2,826,310 | 0 | T | G | 32.5% | 195.8 / 10.7 | 116 | V160G (GTG→GGG) | srlA | glucitol/sorbitol‑specific enzyme IIC component of PTS |
| * | NC_000913 | 3,745,042 | 0 | A | C | 32.2% | 92.5 / 10.1 | 97 | D80A (GAC→GCC) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,862,661 | 0 | T | G | 31.9% | 65.6 / 19.0 | 74 | pseudogene (943/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 3,862,664 | 0 | C | G | 31.9% | 64.2 / 21.4 | 76 | pseudogene (940/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 3,745,019 | 0 | C | G | 30.8% | 138.2 / 27.9 | 107 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 4,571,183 | 0 | A | C | 30.8% | 258.2 / 15.7 | 121 | V131G (GTG→GGG) | yjiR | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| * | NC_000913 | 811,721 | 0 | T | G | 30.7% | 362.7 / 15.4 | 167 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 1,679,304 | 0 | A | C | 30.4% | 275.5 / 22.9 | 115 | Y293S (TAC→TCC) | ydgH | DUF1471 family periplasmic protein |
| * | NC_000913 | 3,862,670 | 0 | T | A | 30.2% | 51.3 / 18.0 | 78 | pseudogene (934/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 3,206,440 | 0 | C | A | 29.9% | 193.8 / 33.3 | 87 | intergenic (‑184/‑23) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 3,862,668 | 0 | A | G | 29.9% | 105.2 / 19.2 | 77 | pseudogene (936/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 743,705 | 0 | T | G | 29.5% | 165.6 / 17.5 | 96 | V38G (GTG→GGG) | ybgJ | putative allophanate hydrolase, subunit 1 |
| * | NC_000913 | 3,586,536 | 0 | A | C | 29.3% | 354.2 / 11.0 | 150 | G96G (GGT→GGG) | ggt | gamma‑glutamyltranspeptidase |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2713829 | 317 (1.140) | 7 (0.030) | 7/350 | 12.5 | 2.4% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 281 (1.080) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 7 (0.030) | 7/358 | 12.6 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 4094338 = | NA (NA) | 26 (0.110) +23 bp |
5/326 | 13.1 | NA | noncoding (23/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | = 4094682 | NA (NA) | noncoding (367/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913 | 225456 = | 117 (0.420) | 11 (0.040) +22 bp |
5/328 | 13.1 | 6.9% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518117 | 222 (0.800) | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala | |||||
| * | ? | NC_000913 | = 2924171 | 303 (1.090) | 6 (0.020) | 6/360 | 13.2 | 1.9% | noncoding (354/369 nt) | csrB | CsrA‑binding sRNA, antagonizing CsrA regulation |
| ? | NC_000913 | = 2924185 | 321 (1.190) | noncoding (340/369 nt) | csrB | CsrA‑binding sRNA, antagonizing CsrA regulation | |||||
| * | ? | NC_000913 | = 2817942 | 232 (0.840) | 7 (0.030) | 5/332 | 13.2 | 3.0% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818078 = | 249 (1.000) | noncoding (58/77 nt) | argZ | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 4082705 | 269 (0.970) | 6 (0.020) | 6/368 | 13.3 | 2.1% | coding (55/903 nt) | fdoH | formate dehydrogenase‑O, Fe‑S subunit |
| ? | NC_000913 | 4082801 = | 297 (1.080) | coding (3022/3051 nt) | fdoG | formate dehydrogenase‑O, large subunit | |||||
| * | ? | NC_000913 | = 4470950 | 322 (1.160) | 5 (0.020) | 5/346 | 13.5 | 1.7% | intergenic (‑37/+36) | ridA/pyrI | enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit |
| ? | NC_000913 | = 4470958 | 291 (1.130) | intergenic (‑45/+28) | ridA/pyrI | enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit | |||||
| * | ? | NC_000913 | 4542682 = | 48 (0.170) | 5 (0.020) | 5/354 | 13.6 | 4.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 152 (0.570) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1457966 = | 181 (0.650) | 6 (0.020) | 5/352 | 13.6 | 3.3% | coding (470/768 nt) | paaF | 2,3‑dehydroadipyl‑CoA hydratase |
| ? | NC_000913 | 1457997 = | 179 (0.680) | coding (501/768 nt) | paaF | 2,3‑dehydroadipyl‑CoA hydratase | |||||