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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,477,265 | 0 | A | C | 38.3% | 104.1 / 31.9 | 81 | L122* (TTA→TGA) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,136,467 | 0 | A | C | 37.8% | 49.2 / 12.2 | 45 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 161,559 | 0 | G | A | 36.8% | 95.5 / 12.8 | 58 | S158L (TCG→TTG) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| * | NC_000913 | 1,922,815 | 0 | C | A | 32.6% | 152.6 / 16.6 | 92 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,054,894 | 0 | G | T | 32.3% | 141.8 / 25.8 | 96 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,097,118 | 0 | C | A | 32.3% | 20.2 / 23.1 | 31 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,269,943 | 0 | G | T | 30.9% | 63.7 / 14.6 | 56 | intergenic (+341/+273) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 847,955 | 0 | G | A | 30.5% | 169.8 / 30.5 | 106 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,249,810 | 0 | C | A | 29.5% | 173.9 / 14.7 | 88 | P86Q (CCG→CAG) | malM | maltose regulon periplasmic protein |
| * | NC_000913 | 3,054,886 | 0 | G | T | 29.0% | 156.6 / 26.4 | 93 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,296,268 | 0 | T | C | 29.0% | 45.3 / 15.0 | 31 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,923,539 | 0 | C | A | 28.3% | 191.2 / 13.9 | 99 | E48* (GAG→TAG) | rsmG | 16S rRNA m(7)G527 methyltransferase |
| * | NC_000913 | 782,194 | 0 | T | G | 28.2% | 182.5 / 14.7 | 103 | L37R (CTA→CGA) | nadA | quinolinate synthase |
| * | NC_000913 | 2,239,994 | 0 | G | T | 27.3% | 247.3 / 16.4 | 110 | R119S (CGT→AGT) | mglB | D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,334,966 | 0 | A | C | 27.1% | 204.0 / 25.1 | 124 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 538,075 | 0 | A | G | 26.6% | 135.4 / 12.1 | 64 | D148G (GAT→GGT) | ybbW | putative allantoin transporter |
| * | NC_000913 | 2,767,445 | 0 | C | A | 26.5% | 197.3 / 10.3 | 84 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,202,004 | 0 | C | A | 26.3% | 146.1 / 55.2 | 76 | G38G (GGC→GGA) | cca | fused CCA tRNA nucleotidyltransferase/phosphohydrolase |
| * | NC_000913 | 2,477,264 | 0 | T | C | 25.9% | 162.5 / 13.9 | 81 | L122L (TTA→TTG) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,226,224 | 0 | G | T | 25.6% | 260.4 / 10.1 | 125 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| 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 | = 2357730 | 103 (1.150) | 10 (0.130) | 10/518 | 5.0 | 10.0% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 90 (1.160) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4606166 | 90 (1.010) | 5 (0.080) | 5/420 | 6.0 | 7.9% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 53 (0.850) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2653419 | 76 (0.850) | 7 (0.090) | 7/548 | 6.4 | 9.1% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 71 (0.870) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2653502 | 91 (1.020) | 6 (0.080) | 6/530 | 6.7 | 7.5% | intergenic (‑47/‑353) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653825 = | 67 (0.850) | intergenic (‑370/‑30) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 781222 | 44 (0.490) | 4 (0.060) | 4/446 | 6.8 | 10.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 33 (0.500) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4542690 | 158 (1.770) | 6 (0.070) | 6/580 | 7.2 | 4.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 111 (1.280) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 155 (1.740) | 6 (0.070) | 6/580 | 7.2 | 4.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 111 (1.280) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3469405 | 116 (1.300) | 4 (0.050) | 4/566 | 8.1 | 3.0% | coding (449/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469715 = | 151 (1.790) | coding (139/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 1251766 | 72 (0.810) | 4 (0.050) | 4/574 | 8.1 | 5.6% | coding (701/1920 nt) | dhaR | DNA‑binding transcriptional dual regulator DhaR |
| ? | NC_000913 | 1252103 = | 65 (0.760) | coding (1038/1920 nt) | dhaR | DNA‑binding transcriptional dual regulator DhaR | |||||
| * | ? | NC_000913 | = 820826 | 2 (0.020) | 3 (0.030) | 3/592 | 8.9 | 60.2% | coding (34/714 nt) | ybhM | Bax1‑I family protein YbhM |
| ? | NC_000913 | 2066159 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||