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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 70,371 | 0 | T | C | 74.8% | 1667.9 / inf | 894 | intergenic (‑323/‑16) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,434 | 0 | C | T | 74.3% | 1582.1 / inf | 882 | N16N (AAC→AAT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,079 | 0 | C | T | 73.4% | 1641.6 / inf | 935 | R231R (CGC→CGT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,082 | 0 | T | C | 72.9% | 1576.8 / inf | 915 | I232I (ATT→ATC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,109 | 0 | T | C | 72.1% | 1581.0 / inf | 955 | T241T (ACT→ACC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,085 | 0 | T | C | 71.8% | 1460.2 / inf | 898 | S233S (AGT→AGC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 566,205 | 0 | T | C | 66.2% | 363.7 / 300.2 | 308 | pseudogene (157/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 71,166 | 0 | T | C | 65.8% | 999.3 / inf | 845 | Y260Y (TAT→TAC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,175 | 0 | A | G | 63.7% | 794.6 / inf | 774 | R263R (CGA→CGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 566,245 | 0 | G | A | 61.8% | 299.4 / inf | 348 | pseudogene (117/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 566,173 | 0 | C | G | 59.2% | 201.9 / inf | 262 | pseudogene (189/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 566,277 | 0 | C | T | 56.5% | 133.2 / inf | 292 | pseudogene (85/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 71,214 | 0 | T | C | 53.1% | 134.6 / inf | 621 | F276F (TTT→TTC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 566,323 | 0 | C | T | 43.2% | 110.6 / 297.3 | 227 | pseudogene (39/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 566,326 | 0 | T | C | 40.1% | 160.6 / 262.7 | 223 | pseudogene (36/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 566,332 | 0 | T | G | 37.1% | 189.9 / 265.3 | 213 | pseudogene (30/264 nt) | exoD | DLP12 prophage; putative exonuclease ExoD |
| * | NC_000913 | 164,581 | 0 | A | C | 34.1% | 71.4 / 27.7 | 91 | intergenic (+47/‑149) | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 164,564 | 0 | A | T | 30.4% | 175.0 / 14.1 | 102 | intergenic (+30/‑166) | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 1,834,470 | 0 | G | C | 28.8% | 150.8 / 21.9 | 76 | E119Q (GAA→CAA) | ydjY | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.7% | 976.2 / inf | 583 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Marginal new junction evidence (lowest skew 10 of 440 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 285801 = | 846 (4.990) | 26 (0.160) | 13/286 | 2.6 | 3.1% | coding (407/1383 nt) | yagG | putative D‑xylonate transporter YagG |
| ? | NC_000913 | 285858 = | 835 (5.130) | coding (464/1383 nt) | yagG | putative D‑xylonate transporter YagG | |||||
| * | ? | NC_000913 | = 3885280 | 510 (3.010) | 26 (0.160) | 12/288 | 2.7 | 5.0% | coding (205/1647 nt) | yidC | membrane protein insertase YidC |
| ? | NC_000913 | = 3885315 | 492 (3.000) | coding (240/1647 nt) | yidC | membrane protein insertase YidC | |||||
| * | ? | NC_000913 | = 3790299 | 221 (1.300) | 14 (0.090) | 12/280 | 2.7 | 6.1% | intergenic (‑218/+21) | waaH/tdh | UDP‑glucuronate:LPS(HepIII) glycosyltransferase/threonine dehydrogenase |
| ? | NC_000913 | = 3790303 | 221 (1.390) | intergenic (‑222/+17) | waaH/tdh | UDP‑glucuronate:LPS(HepIII) glycosyltransferase/threonine dehydrogenase | |||||
| * | ? | NC_000913 | 4321860 = | 1268 (7.480) | 15 (0.090) | 10/286 | 2.9 | 1.2% | coding (563/726 nt) | phnF | putative transcriptional regulator PhnF |
| ? | NC_000913 | 4321892 = | 1157 (7.120) | coding (531/726 nt) | phnF | putative transcriptional regulator PhnF | |||||
| * | ? | NC_000913 | = 4168373 | 163 (0.960) | 7 (0.070) +66 bp |
5/166 | 2.9 | 4.9% | noncoding (2/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | = 4209753 | 324 (1.910) | intergenic (+65/‑21) | rrsE/gltV | 16S ribosomal RNA/tRNA‑Glu | |||||
| * | ? | NC_000913 | 3873646 = | 824 (4.860) | 25 (0.150) | 10/284 | 2.9 | 3.1% | coding (829/879 nt) | dgoK | 2‑dehydro‑3‑deoxygalactonokinase |
| ? | NC_000913 | 3873729 = | 776 (4.810) | coding (746/879 nt) | dgoK | 2‑dehydro‑3‑deoxygalactonokinase | |||||
| * | ? | NC_000913 | 3854880 = | 807 (4.760) | 20 (0.130) | 10/280 | 2.9 | 2.6% | coding (959/1185 nt) | emrD | multidrug efflux pump EmrD |
| ? | NC_000913 | 3854940 = | 719 (4.520) | coding (1019/1185 nt) | emrD | multidrug efflux pump EmrD | |||||
| * | ? | NC_000913 | 4320612 = | 1258 (7.420) | 19 (0.120) | 9/288 | 3.1 | 1.6% | coding (52/1065 nt) | phnI | carbon‑phosphorus lyase core complex subunit PhnI |
| ? | NC_000913 | 4320644 = | 1173 (7.160) | coding (20/1065 nt) | phnI | carbon‑phosphorus lyase core complex subunit PhnI | |||||
| * | ? | NC_000913 | = 3854228 | 828 (4.890) | 18 (0.110) | 9/284 | 3.1 | 2.3% | coding (307/1185 nt) | emrD | multidrug efflux pump EmrD |
| ? | NC_000913 | = 3854256 | 738 (4.570) | coding (335/1185 nt) | emrD | multidrug efflux pump EmrD | |||||
| * | ? | NC_000913 | 3124692 = | 451 (2.660) | 12 (0.070) | 9/290 | 3.1 | 2.6% | coding (768/1224 nt) | glcF | glycolate dehydrogenase, putative iron‑sulfur subunit |
| ? | NC_000913 | 3124729 = | 444 (2.690) | coding (731/1224 nt) | glcF | glycolate dehydrogenase, putative iron‑sulfur subunit | |||||