mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 53 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 56.9% | ‑6.3 / 118.7 | 102 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 54.8% | 13.1 / 104.2 | 84 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 45.7% | 50.1 / 135.5 | 105 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 44.3% | 56.5 / 111.0 | 98 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,353,192 | 0 | C | A | 40.0% | 39.4 / 11.1 | 37 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 4,340,081 | 0 | A | G | 39.3% | 20.6 / 25.7 | 30 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,076 | 0 | G | C | 37.0% | 25.6 / 26.5 | 28 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,083 | 0 | A | G | 35.7% | 25.9 / 22.7 | 30 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,075 | 0 | A | T | 34.5% | 24.1 / 20.7 | 31 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,082 | 0 | C | T | 33.3% | 32.6 / 20.2 | 30 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,273,066 | 0 | A | T | 31.0% | 61.6 / 43.3 | 60 | intergenic (+31/+260) | PP_2003/PP_2004 | hypothetical protein/AraC family transcriptional regulator |
| * | NC_002947 | 4,340,084 | 0 | C | T | 31.0% | 38.4 / 18.1 | 30 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,090 | 0 | A | T | 30.3% | 44.3 / 21.2 | 35 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,273,070 | 0 | C | G | 30.0% | 96.8 / 47.4 | 60 | intergenic (+35/+256) | PP_2003/PP_2004 | hypothetical protein/AraC family transcriptional regulator |
| * | NC_002947 | 4,340,089 | 0 | G | C | 29.7% | 48.0 / 24.3 | 37 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,273,062 | 0 | C | G | 29.5% | 107.9 / 37.8 | 61 | intergenic (+27/+264) | PP_2003/PP_2004 | hypothetical protein/AraC family transcriptional regulator |
| * | NC_002947 | 196,351 | 0 | C | G | 28.9% | 207.8 / 103.9 | 135 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,740,467 | 0 | T | G | 28.8% | 58.1 / 34.6 | 52 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 3,287,276 | 0 | T | C | 26.9% | 33.2 / 14.1 | 27 | intergenic (+17/+24) | PP_2889/xthA | transmembrane regulator PrtR/exodeoxyribonuclease III/apurinic/apyrimidinic endodeoxyribonuclease VI |
| * | NC_002947 | 1,703,248 | 0 | A | G | 26.5% | 74.1 / 30.0 | 53 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 596 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 652782 | 47 (0.700) | 13 (0.230) | 12/234 | 5.1 | 38.7% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808179 | 3 (0.040) | 28 (0.450) | 11/250 | 5.8 | 46.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 62 (1.010) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 2086450 | NA (NA) | 14 (0.220) | 12/262 | 5.8 | NA | coding (565/1302 nt) | PP_1865 | transposase |
| ? | NC_002947 | = 2086464 | NA (NA) | coding (579/1302 nt) | PP_1865 | transposase | |||||
| * | ? | NC_002947 | 742597 = | NA (NA) | 19 (0.290) | 12/268 | 5.9 | NA | coding (698/1422 nt) | PP_0635 | group II intron‑encoding maturase |
| ? | NC_002947 | 742657 = | NA (NA) | coding (758/1422 nt) | PP_0635 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 4647557 = | 41 (0.610) | 7 (0.140) | 7/196 | 6.0 | 19.6% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647665 = | 28 (0.580) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 742915 = | NA (NA) | 15 (0.230) | 11/262 | 6.1 | NA | coding (1016/1422 nt) | PP_0635 | group II intron‑encoding maturase |
| ? | NC_002947 | 742945 = | NA (NA) | coding (1046/1422 nt) | PP_0635 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 278743 = | 66 (0.980) | 13 (0.210) | 10/246 | 6.1 | 18.4% | intergenic (‑238/+76) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| ? | NC_002947 | 278794 = | 56 (0.920) | intergenic (‑289/+25) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947 | 1426800 = | NA (NA) | 19 (0.290) | 11/268 | 6.3 | NA | coding (698/1422 nt) | PP_1250 | group II intron‑encoding maturase |
| ? | NC_002947 | 1426860 = | NA (NA) | coding (758/1422 nt) | PP_1250 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 4140139 = | 76 (1.120) | 10 (0.160) | 10/258 | 6.4 | 12.4% | intergenic (+31/‑234) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein |
| ? | NC_002947 | 4140178 = | 70 (1.100) | intergenic (+70/‑195) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein | |||||
| * | ? | NC_002947 | 1731163 = | 62 (0.920) | 7 (0.130) | 7/218 | 6.6 | 13.2% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731255 = | 43 (0.800) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||