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 33 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,541,921 | 0 | G | A | 63.7% | 96.1 / 95.6 | 91 | W505* (TGG→TGA) | feoB | Fe(2(+)) transporter FeoB |
| * | NC_000913 | 1,922,815 | 0 | C | A | 41.3% | 108.9 / 36.9 | 104 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,477,265 | 0 | A | C | 35.1% | 131.4 / 19.4 | 77 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.6% | 111.7 / 24.4 | 81 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 34.5% | 182.1 / 23.9 | 110 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 33.9% | 202.0 / 22.6 | 118 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,054,886 | 0 | G | T | 33.8% | 122.7 / 28.1 | 80 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,611,507 | 0 | G | T | 33.3% | 159.3 / 11.1 | 93 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 2,288,418 | 0 | G | T | 31.5% | 276.2 / 23.2 | 143 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 1,334,966 | 0 | A | C | 31.1% | 243.0 / 24.5 | 148 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,741,871 | 0 | G | T | 30.6% | 164.1 / 12.8 | 98 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,945,526 | 0 | G | T | 28.9% | 112.1 / 11.7 | 76 | P151T (CCT→ACT) | ruvA | Holliday junction branch migration complex subunit RuvA |
| * | NC_000913 | 1,470,627 | 0 | C | A | 28.8% | 262.9 / 16.8 | 125 | pseudogene (109/3495 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 1,434,642 | 0 | G | A | 28.3% | 334.0 / 156.6 | 182 | intergenic (‑236/+543) | ynaM/uspF | protein YnaM/universal stress protein F |
| * | NC_000913 | 1,466,438 | 0 | T | G | 27.7% | 67.5 / 28.1 | 48 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 1,097,118 | 0 | C | A | 27.6% | 45.3 / 12.7 | 29 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 782,194 | 0 | T | G | 25.6% | 226.8 / 18.1 | 121 | L37R (CTA→CGA) | nadA | quinolinate synthase |
| * | NC_000913 | 847,955 | 0 | G | A | 25.5% | 180.7 / 25.6 | 106 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,466,432 | 0 | A | G | 25.0% | 84.2 / 24.0 | 48 | pseudogene (1041/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 4,296,268 | 0 | T | C | 25.0% | 65.3 / 22.5 | 40 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 25 (0.270) | 22/598 | 3.4 | 15.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3269433 = | 136 (1.460) | coding (1019/1188 nt) | yhaC | uncharacterized protein YhaC | |||||
| * | ? | NC_000913 | = 889531 | 127 (1.370) | 27 (0.290) | 21/594 | 3.6 | 17.5% | coding (289/1686 nt) | ybjL | putative transport protein YbjL |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3269436 | 131 (1.410) | 23 (0.250) | 20/598 | 3.8 | 14.9% | coding (1022/1188 nt) | yhaC | uncharacterized protein YhaC |
| ? | NC_000913 | = 3366750 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 270541 = | NA (NA) | 18 (0.190) | 16/598 | 4.7 | 12.6% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 889530 = | 125 (1.340) | coding (290/1686 nt) | ybjL | putative transport protein YbjL | |||||
| * | ? | NC_000913 | = 4542690 | 136 (1.460) | 17 (0.190) | 15/580 | 4.8 | 12.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 104 (1.150) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 125 (1.340) | 15 (0.170) | 13/580 | 5.3 | 11.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 106 (1.170) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648146 | 86 (0.920) | 9 (0.120) | 8/482 | 6.0 | 11.5% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 69 (0.920) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781222 | 38 (0.410) | 7 (0.100) | 6/446 | 6.4 | 14.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 54 (0.780) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 280111 | NA (NA) | 14 (0.150) | 10/594 | 6.4 | 9.9% | noncoding (181/181 nt) | IS30 | repeat region |
| ? | NC_000913 | = 889531 | 127 (1.370) | coding (289/1686 nt) | ybjL | putative transport protein YbjL | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 14 (0.150) | 10/594 | 6.4 | 9.9% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 889531 | 127 (1.370) | coding (289/1686 nt) | ybjL | putative transport protein YbjL | |||||