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 44 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,066,555 | 0 | C | T | 59.1% | ‑3.6 / 26.8 | 22 | R256H (CGC→CAC) | insH‑6 | CP4‑44 prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 876,898 | 0 | C | T | 58.9% | 263.2 / inf | 334 | G380S (GGC→AGC) | rimO | ribosomal protein S12 methylthiotransferase RimO |
| * | NC_000913 | 2,936,783 | 0 | T | C | 57.6% | 175.8 / inf | 288 | G400G (GGT→GGC) | fucI | L‑fucose isomerase |
| * | NC_000913 | 4,466,732 | 0 | T | C | 57.1% | 176.2 / inf | 337 | D172G (GAC→GGC) | treR | DNA‑binding transcriptional repressor TreR |
| * | NC_000913 | 1,614,450 | 0 | T | C | 56.2% | 116.5 / inf | 249 | Q85R (CAG→CGG) | sad | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| * | NC_000913 | 888,037 | 0 | A | G | 56.2% | 163.0 / inf | 325 | noncoding (21/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,860,887 | 0 | T | C | 55.9% | 148.5 / inf | 338 | S116S (TCA→TCG) | ygbI | putative DeoR‑type DNA‑binding transcriptional regulator YgbI |
| * | NC_000913 | 2,083,005 | 0 | T | C | 55.5% | 128.4 / inf | 299 | F84L (TTT→CTT) | sbcB | exodeoxyribonuclease I |
| * | NC_000913 | 1,310,614 | 0 | T | C | 54.0% | 110.7 / inf | 328 | G84G (GGA→GGG) | yciI | protein YciI |
| * | NC_000913 | 245,703 | 0 | A | G | 53.8% | 139.8 / inf | 403 | Y35H (TAT→CAT) | yafK | L,D‑transpeptidase domain‑containing protein YafK |
| * | NC_000913 | 3,226,666 | 0 | G | . | 53.5% | inf / inf | 357 | coding (433/1434 nt) | ygjI | putative transporter YgjI |
| * | NC_000913 | 1,034,524 | 0 | A | G | 49.7% | 21.9 / inf | 316 | D424G (GAT→GGT) | hyaB | hydrogenase 1 large subunit |
| * | NC_000913 | 3,202,202 | 0 | C | T | 49.1% | 36.0 / inf | 328 | G104G (GGC→GGT) | cca | fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase and phosphatase |
| * | NC_000913 | 2,806,207 | 0 | T | C | 47.0% | 112.8 / inf | 404 | S66S (AGT→AGC) | proW | glycine betaine ABC transporter membrane subunit ProW |
| * | NC_000913 | 4,330,240 | 0 | T | C | 46.7% | 138.1 / inf | 422 | intergenic (+2/‑262) | yjcZ/proP | uncharacterized protein YjcZ/osmolyte:H(+) symporter ProP |
| * | NC_000913 | 3,728,110 | 2 | . | C | 45.3% | 2.6 / 126.3 | 53 | coding (1262/1455 nt) | xylB | xylulokinase |
| * | NC_000913 | 3,030,908 | 0 | T | C | 44.3% | 200.3 / inf | 359 | E8E (GAA→GAG) | ygfT | fused putative oxidoreductase, Fe‑S subunit and nucleotide‑binding subunit |
| * | NC_000913 | 839,579 | 0 | A | G | 44.1% | 159.4 / inf | 304 | G651G (GGT→GGC) | fiu | putative iron siderophore outer membrane transporter |
| * | NC_000913 | 1,594,248 | 1 | . | C | 43.6% | 52.4 / inf | 237 | pseudogene (3839/5422 nt) | yneO | AIDA‑I family autotransporter YneO |
| * | NC_000913 | 3,178,015 | 0 | G | A | 43.4% | 188.3 / inf | 357 | intergenic (‑105/‑100) | nudF/tolC | ADP‑sugar pyrophosphatase/outer membrane channel TolC |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 169 (0.470) | 125 (0.420) | 83/162 | 6.5 | 45.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 165 (0.550) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 3728110 | 29 (0.090) | 162 (0.460) +CCC |
83/172 | 7.6 | 84.4% | coding (1262/1455 nt) | xylB | xylulokinase |
| ? | NC_000913 | 3728111 = | 30 (0.080) | coding (1261/1455 nt) | xylB | xylulokinase | |||||
| * | ? | NC_000913 | = 71350 | 418 (1.160) | 112 (0.320) | 56/188 | 16.3 | 35.6% | intergenic (+85/‑1) | araC/yabI | DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI |
| ? | NC_000913 | = 2857042 | 0 (0.000) | intergenic (‑236/‑51) | ygbA/mutS | protein YgbA/DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | = 1209618 | 165 (0.460) | 29 (0.100) | 16/164 | 30.2 | 10.8% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 338 (1.110) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 28 (0.080) | 19/194 | 31.8 | 5.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4503695 | 454 (1.260) | intergenic (‑264/‑363) | insG/yjhB | KpLE2 phage‑like element; IS4 putative transposase/putative sialic acid transporter | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 16 (0.040) | 14/194 | 34.8 | 3.5% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4503687 = | 445 (1.240) | intergenic (‑256/‑371) | insG/yjhB | KpLE2 phage‑like element; IS4 putative transposase/putative sialic acid transporter | |||||
| * | ? | NC_000913 | = 4542690 | 469 (1.300) | 9 (0.030) | 9/176 | 36.5 | 2.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 396 (1.210) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 473 (1.310) | 10 (0.030) | 9/176 | 36.5 | 2.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 396 (1.210) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 290634 = | NA (NA) | 11 (0.030) | 10/194 | 37.6 | 2.4% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4503695 | 454 (1.260) | intergenic (‑264/‑363) | insG/yjhB | KpLE2 phage‑like element; IS4 putative transposase/putative sialic acid transporter | |||||
| * | ? | NC_000913 | 1049778 = | NA (NA) | 7 (0.020) | 5/186 | 41.1 | 1.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4503687 = | 445 (1.240) | intergenic (‑256/‑371) | insG/yjhB | KpLE2 phage‑like element; IS4 putative transposase/putative sialic acid transporter | |||||