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 | 4,208,132 | 0 | G | A | 76.7% | 224.6 / 101.5 | 150 | intergenic (‑600/‑15) | purH/rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| * | NC_000913 | 2,477,265 | 0 | A | C | 47.4% | 101.8 / 37.6 | 95 | L122* (TTA→TGA) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,097,158 | 0 | C | T | 45.5% | ‑3.2 / 25.1 | 22 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 58,065 | 0 | C | A | 38.1% | 125.2 / 39.6 | 105 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 4,296,191 | 0 | A | C | 37.0% | 27.1 / 15.5 | 27 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,767,445 | 0 | C | A | 36.1% | 130.0 / 12.8 | 84 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 332,975 | 0 | C | A | 35.3% | 124.1 / 11.5 | 85 | S202* (TCG→TAG) | pdeL | DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 2,477,300 | 0 | C | A | 35.0% | 184.4 / 10.3 | 102 | R110R (CGG→CGT) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,886 | 0 | G | T | 34.1% | 144.2 / 26.7 | 91 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,943,634 | 0 | A | G | 33.5% | 152.8 / 164.2 | 161 | intergenic (+124/‑70) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 33.1% | 213.4 / 21.5 | 136 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,054,894 | 0 | G | T | 32.6% | 117.9 / 29.9 | 90 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,334,966 | 0 | A | C | 30.6% | 256.4 / 26.2 | 147 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,477,282 | 0 | G | A | 30.2% | 179.4 / 14.9 | 100 | C116C (TGC→TGT) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 847,955 | 0 | G | A | 29.9% | 167.4 / 37.4 | 117 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,477,264 | 0 | T | C | 28.7% | 176.5 / 16.4 | 96 | L122L (TTA→TTG) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,365,840 | 0 | T | G | 28.2% | 218.3 / 19.0 | 149 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 4,136,467 | 0 | A | C | 28.0% | 151.9 / 10.8 | 75 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 710,830 | 0 | G | T | 27.1% | 195.1 / 13.2 | 96 | intergenic (‑105/+105) | uof/fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| * | NC_000913 | 3,226,224 | 0 | G | T | 26.7% | 260.3 / 17.8 | 135 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 148 (1.590) | 23 (0.260) | 21/580 | 3.2 | 14.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 139 (1.540) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 140 (1.510) | 18 (0.200) | 16/580 | 4.2 | 11.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 141 (1.570) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 16 (0.170) | 13/598 | 5.1 | 12.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3890222 = | 111 (1.200) | intergenic (+77/‑14) | tnaA/tnaB | tryptophanase/tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 14 (0.150) | 13/598 | 5.1 | 9.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 676373 | 140 (1.510) | coding (175/978 nt) | ybeQ | Sel1 repeat‑containing protein YbeQ | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 14 (0.150) | 12/598 | 5.3 | 10.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3890225 | 115 (1.240) | intergenic (+80/‑11) | tnaA/tnaB | tryptophanase/tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 11 (0.120) | 10/598 | 6.0 | 10.6% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2317256 = | 93 (1.000) | coding (2621/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | = 781222 | 51 (0.550) | 6 (0.090) | 6/446 | 6.0 | 10.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 66 (0.950) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 696741 | 57 (0.610) | 8 (0.120) | 6/442 | 6.0 | 14.9% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 49 (0.710) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 253554 | 79 (0.850) | 12 (0.130) | 10/598 | 6.0 | 13.2% | intergenic (+393/+705) | yafP/pepD | putative N‑acetyltransferase YafP/peptidase D |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 10 (0.110) | 9/598 | 6.3 | 9.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2317260 | 97 (1.040) | coding (2617/2850 nt) | rcsC | histidine kinase RcsC | |||||