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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,037,496 | 0 | A | T | 45.5% | 68.4 / 253.0 | 135 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 44.3% | 125.7 / 22.3 | 106 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,097,118 | 0 | C | A | 35.3% | 12.7 / 13.4 | 17 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,502,772 | 0 | G | A | 32.4% | 89.1 / 21.0 | 69 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,427,992 | 0 | G | T | 32.2% | 181.5 / 13.8 | 121 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 1,502,770 | 0 | T | C | 31.9% | 86.8 / 24.5 | 69 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 85,651 | 0 | G | T | 30.9% | 133.0 / 12.2 | 94 | E8* (GAG→TAG) | ilvI | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| * | NC_000913 | 3,054,886 | 0 | G | T | 29.8% | 101.7 / 13.5 | 67 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.7% | 173.7 / 14.6 | 101 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,477,265 | 0 | A | C | 27.9% | 103.2 / 10.5 | 61 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,926,595 | 0 | C | A | 27.7% | 141.8 / 13.2 | 83 | E137* (GAG→TAG) | asnC | DNA‑binding transcriptional dual regulator AsnC |
| * | NC_000913 | 4,249,810 | 0 | C | A | 27.4% | 124.8 / 15.7 | 73 | P86Q (CCG→CAG) | malM | maltose regulon periplasmic protein |
| * | NC_000913 | 3,620,844 | 0 | T | C | 27.3% | 15.7 / 13.2 | 22 | R551R (CGT→CGC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 1,480,719 | 0 | G | T | 27.0% | 136.8 / 10.9 | 74 | E528* (GAG→TAG) | ynbC | hydrolase/methyltransferase domain‑containing protein YnbC |
| * | NC_000913 | 4,296,268 | 0 | T | C | 26.9% | 37.9 / 11.7 | 26 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 847,955 | 0 | G | A | 26.7% | 177.9 / 32.6 | 105 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,360,965 | 0 | C | A | 26.5% | 228.1 / 16.0 | 118 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,490,240 | 0 | G | T | 26.1% | 162.5 / 12.3 | 92 | intergenic (‑54/+16) | yfdV/oxc | putative transport protein YfdV/oxalyl‑CoA decarboxylase |
| * | NC_000913 | 3,620,859 | 0 | C | T | 25.9% | 27.9 / 12.9 | 27 | R556R (CGC→CGT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,862 | 0 | C | T | 25.9% | 24.5 / 15.9 | 27 | F557F (TTC→TTT) | rhsB | rhs element protein RhsB |
| Marginal new junction evidence (lowest skew 10 of 41 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2653419 | 64 (0.830) | 14 (0.200) | 13/538 | 3.1 | 17.8% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 71 (1.010) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2947467 | 59 (0.770) | 10 (0.180) | 7/422 | 3.8 | 17.5% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 52 (0.940) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2357690 | 88 (1.150) | 8 (0.110) | 8/538 | 4.5 | 9.3% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 76 (1.080) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4542690 | 159 (2.070) | 13 (0.170) | 8/570 | 4.7 | 9.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 103 (1.380) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 148 (1.930) | 12 (0.160) | 8/570 | 4.7 | 8.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 105 (1.410) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 781446 | 45 (0.590) | 5 (0.090) | 5/432 | 4.7 | 14.1% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 28 (0.500) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 359900 | 1358 (17.680) | 8 (0.110) | 8/574 | 4.7 | 0.66% | coding (412/471 nt) | cynS | cyanase |
| ? | NC_000913 | 360159 = | 1076 (14.350) | coding (168/1155 nt) | cynX | cyanate transporter | |||||
| * | ? | NC_000913 | = 4392437 | 54 (0.700) | 4 (0.070) | 4/432 | 5.2 | 7.8% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 55 (0.970) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 2357652 | 83 (1.080) | 5 (0.070) +GCGGCAGGAAGGACG |
5/558 | 5.8 | 5.9% | coding (749/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357851 = | 85 (1.110) | intergenic (+48/+191) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3469405 | 102 (1.330) | 4 (0.060) | 4/556 | 6.2 | 3.9% | coding (449/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469715 = | 101 (1.390) | coding (139/2694 nt) | chiA | endochitinase | |||||