mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,911,533 | 0 | C | A | 42.6% | 139.2 / 32.9 | 129 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,620,844 | 0 | T | C | 41.7% | ‑2.1 / 11.1 | 12 | R551R (CGT→CGC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,859 | 0 | C | T | 38.5% | ‑0.4 / 10.9 | 13 | R556R (CGC→CGT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,226,224 | 0 | G | T | 37.2% | 184.8 / 11.9 | 113 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| * | NC_000913 | 1,427,992 | 0 | G | T | 37.1% | 201.6 / 24.5 | 140 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,433,340 | 0 | G | T | 35.6% | 150.1 / 18.2 | 90 | S196Y (TCC→TAC) | accD | acetyl‑CoA carboxyltransferase subunit beta |
| * | NC_000913 | 4,037,496 | 0 | A | T | 35.6% | 237.3 / 259.4 | 182 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 58,065 | 0 | C | A | 35.5% | 142.6 / 22.2 | 93 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,351,463 | 0 | C | A | 35.4% | 99.6 / 12.4 | 82 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 12,152 | 0 | G | T | 35.3% | 156.4 / 17.3 | 119 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 4,427,822 | 0 | C | A | 34.3% | 195.9 / 10.9 | 108 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 3,741,871 | 0 | G | T | 33.3% | 145.3 / 13.3 | 96 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,856,087 | 0 | G | T | 32.4% | 170.6 / 15.7 | 102 | E584* (GAG→TAG) | fhlA | DNA‑binding transcriptional activator FhlA |
| * | NC_000913 | 1,631,903 | 0 | G | T | 32.1% | 173.6 / 10.3 | 106 | S128Y (TCC→TAC) | ydfJ | putative transporter YdfJ |
| * | NC_000913 | 3,054,886 | 0 | G | T | 31.3% | 135.3 / 17.2 | 83 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 332,975 | 0 | C | A | 30.7% | 200.4 / 19.3 | 127 | S202* (TCG→TAG) | pdeL | DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 430,299 | 0 | C | A | 30.3% | 165.8 / 10.7 | 91 | F265L (TTC→TTA) | secF | Sec translocon accessory complex subunit SecF |
| * | NC_000913 | 3,923,539 | 0 | C | A | 28.9% | 160.0 / 12.0 | 97 | E48* (GAG→TAG) | rsmG | 16S rRNA m(7)G527 methyltransferase |
| * | NC_000913 | 2,818,324 | 0 | G | A | 28.6% | 93.5 / 37.3 | 56 | intergenic (‑50/+149) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| * | NC_000913 | 2,239,994 | 0 | G | T | 28.2% | 229.8 / 11.5 | 110 | R119S (CGT→AGT) | mglB | D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 133 (1.430) | 17 (0.190) | 13/566 | 4.3 | 11.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 127 (1.410) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4606166 | 124 (1.340) | 8 (0.120) | 7/406 | 4.7 | 9.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 64 (0.990) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 780918 | 69 (0.740) | 8 (0.120) | 6/432 | 5.4 | 15.5% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 36 (0.530) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 1286906 | 58 (0.630) | 9 (0.100) | 8/544 | 5.7 | 14.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 52 (0.600) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2653419 | 78 (0.840) | 7 (0.080) | 7/534 | 6.0 | 8.0% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 89 (1.050) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2357690 | 95 (1.020) | 8 (0.090) | 6/534 | 6.4 | 8.8% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 80 (0.940) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1287084 | 56 (0.600) | 9 (0.100) | 5/544 | 6.9 | 14.7% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 52 (0.600) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4176887 | NA (NA) | 5 (0.060) | 5/558 | 7.0 | 6.3% | coding (944/1185 nt) | tufB | translation elongation factor Tu 2 |
| ? | NC_000913 | 4177077 = | 78 (0.840) | coding (1134/1185 nt) | tufB | translation elongation factor Tu 2 | |||||
| * | ? | NC_000913 | = 4094350 | 58 (0.630) | 4 (0.050) | 4/502 | 7.0 | 6.6% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 64 (0.800) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 4542690 | 148 (1.600) | 5 (0.060) | 5/566 | 7.1 | 3.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 127 (1.410) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||