mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 130 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006881 | 3,735,928 | 0 | G | T | 60.0% | ‑4.2 / 17.8 | 27 | L60I (CTA→ATA) | U712_19255 | Quinol oxidase subunit 2 |
| * | CP006881 | 3,735,920 | 0 | G | T | 52.9% | 12.8 / 33.9 | 35 | T62T (ACC→ACA) | U712_19255 | Quinol oxidase subunit 2 |
| * | CP006881 | 2,992,459 | 0 | T | G | 50.0% | ‑6.3 / 15.0 | 22 | noncoding (2315/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 2,992,535 | 0 | A | C | 48.1% | ‑5.4 / 26.0 | 60 | noncoding (2239/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 3,735,903 | 0 | T | G | 46.9% | 24.0 / 22.7 | 49 | Y68S (TAC→TCC) ‡ | U712_19255 | Quinol oxidase subunit 2 |
| * | CP006881 | 3,735,904 | 0 | A | T | 44.9% | 14.0 / 30.9 | 49 | Y68N (TAC→AAC) ‡ | U712_19255 | Quinol oxidase subunit 2 |
| * | CP006881 | 223,388 | 0 | G | T | 42.6% | 55.9 / 27.7 | 54 | Q203K (CAA→AAA) | U712_01030 | putative serine/threonine‑protein kinase ybdM |
| * | CP006881 | 571,253 | 0 | A | C | 39.3% | 37.9 / 29.5 | 56 | intergenic (‑145/+27) | U712_02810/U712_02815 | putative transporter YdgF/Protein dinB |
| * | CP006881 | 498,572 | 0 | T | G | 38.6% | 33.2 / 17.6 | 44 | E196A (GAG→GCG) | U712_02345 | Putative rhomboid protease ydcA |
| * | CP006881 | 3,151,131 | 0 | T | G | 37.5% | 35.9 / 24.6 | 49 | F39C (TTT→TGT) | U712_16180 | Uric acid degradation bifunctional protein PucL |
| * | CP006881 | 223,378 | 0 | C | T | 37.2% | 47.1 / 31.5 | 56 | G206E (GGA→GAA) | U712_01030 | putative serine/threonine‑protein kinase ybdM |
| * | CP006881 | 3,921,951 | 0 | A | C | 37.1% | 67.4 / 36.9 | 89 | L30R (CTG→CGG) | U712_20210 | Uncharacterized protein yxaJ |
| * | CP006881 | 223,371 | 0 | C | G | 36.7% | 110.8 / 14.9 | 65 | K208N (AAG→AAC) | U712_01030 | putative serine/threonine‑protein kinase ybdM |
| * | CP006881 | 3,735,909 | 0 | A | T | 36.2% | 34.7 / 19.8 | 47 | V66E (GTA→GAA) | U712_19255 | Quinol oxidase subunit 2 |
| * | CP006881 | 3,402,413 | 0 | A | C | 35.7% | 39.6 / 13.7 | 42 | F166V (TTT→GTT) | U712_17465 | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino] imidazole‑4‑carboxamide isomerase |
| * | CP006881 | 1,566,917 | 0 | G | C | 35.6% | 51.8 / 17.3 | 45 | R34T (AGA→ACA) | U712_08065 | Sporulation sigma‑E factor‑processing peptidase |
| * | CP006881 | 2,136,054 | 0 | C | A | 35.4% | 72.9 / 22.6 | 66 | V415L (GTA→TTA) | U712_10675 | Xanthine permease |
| * | CP006881 | 3,303,024 | 0 | T | A | 34.9% | ‑2.7 / 12.2 | 43 | L99F (TTA→TTT) | U712_16990 | Arabinose‑proton symporter |
| * | CP006881 | 238,237 | 0 | T | G | 34.8% | 90.7 / 37.9 | 89 | N33H (AAC→CAC) | U712_01105 | Uncharacterized protein ybfE |
| * | CP006881 | 3,592,477 | 0 | G | C | 34.8% | 138.7 / 54.9 | 91 | intergenic (‑61/+33) | U712_18475/U712_18480 | Uncharacterized protein ywmE/Uncharacterized protein ywmD |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006881 | = 2930156 | 123 (1.120) | 4 (0.040) | 4/234 | 6.6 | 3.1% | coding (894/1005 nt) | U712_15090 | Sensor protein BceS |
| ? | CP006881 | = 3704038 | 132 (1.290) | coding (841/1020 nt) | U712_19080 | Spore coat polysaccharide biosynthesis protein spsG | |||||
| * | ? | CP006881 | = 1688810 | 147 (1.340) | 3 (0.030) | 3/252 | 7.5 | 2.4% | coding (443/1695 nt) | U712_08700 | Prolyl‑tRNA synthetase |
| ? | CP006881 | 3956350 = | 96 (0.870) | coding (292/1164 nt) | U712_20390 | Uncharacterized protein yycP | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5551 | 2768 (0.800) | 25 (0.010) | 20/242 | 16.8 | 0.93% | intergenic (+820/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9889 = | NA (NA) | intergenic (+5158/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 2789 (0.810) | 11 (0.000) | 11/246 | 20.5 | 0.39% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 2888 (0.860) | intergenic (+4801/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 3854 = | 132 (0.040) | 16 (0.000) +A |
7/250 | 22.8 | 19.6% | intergenic (+139/‑17) | eryR/ampR | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 11568 | 0 (0.000) | intergenic (+6837/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 6642 | 2984 (0.870) | 9 (0.000) | 4/242 | 24.6 | 0.39% | intergenic (+1911/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 6733 = | 1696 (0.510) | intergenic (+2002/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 248 = | 6284 (1.830) | 3 (0.000) | 3/246 | 25.6 | 0.054% | intergenic (–/‑2730) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 586 | 4925 (1.470) | intergenic (–/‑2392) | –/eryR | –/– | |||||