mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 157 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,725 | 0 | A | G | 52.0% | ‑5.3 / inf | 293 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,353,698 | 0 | A | G | 50.3% | 120.9 / inf | 370 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,332,076 | 0 | C | T | 49.9% | 166.6 / inf | 374 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 40.2% | 340.5 / inf | 406 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,798,394 | 0 | C | G | 40.0% | 31.1 / 35.7 | 30 | F207L (TTC→TTG) | bamA‑I | outer membrane protein assembly factor |
| * | NC_002947 | 1,549,495 | 0 | T | G | 39.9% | 138.8 / 251.8 | 203 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,287,762 | 0 | T | G | 38.0% | 115.9 / 183.4 | 159 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,549,492 | 0 | G | C | 37.3% | 201.5 / 211.5 | 186 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,708,239 | 0 | A | G | 36.5% | 203.0 / 193.4 | 213 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 1,018,200 | 0 | A | T | 35.6% | 183.4 / 160.5 | 165 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,549,485 | 0 | C | G | 35.5% | 227.5 / 209.1 | 186 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,549,490 | 0 | C | G | 35.5% | 224.4 / 210.8 | 186 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,345,068 | 0 | A | T | 35.1% | 116.1 / 90.5 | 98 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,018,194 | 0 | G | C | 35.0% | 213.1 / 178.0 | 162 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 407,407 | 0 | G | A | 34.8% | 238.3 / 213.0 | 226 | P201S (CCG→TCG) | aceF | AceF‑S‑acetyldihydrolipoate |
| * | NC_002947 | 1,549,480 | 0 | C | A | 34.7% | 211.1 / 197.9 | 193 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,018,193 | 0 | G | C | 34.6% | 225.7 / 175.6 | 162 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 4,813,174 | 0 | A | C | 34.5% | 56.5 / 57.2 | 55 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,175 | 0 | A | G | 34.5% | 55.1 / 48.9 | 55 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 1,549,483 | 0 | G | C | 34.5% | 239.1 / 213.1 | 194 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 371 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 42 (0.180) | 104 (0.580) | 47/224 | 4.5 | 55.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 132 (0.730) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 36 (0.150) | 85 (0.390) | 45/270 | 6.8 | 48.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 150 (0.690) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 204 (0.860) | 71 (0.350) | 36/254 | 8.1 | 44.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4813173 | 36 (0.150) | 54 (0.260) | 24/254 | 11.6 | 34.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 171 (0.840) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4591049 | 93 (0.390) | 39 (0.220) | 19/218 | 11.6 | 40.5% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4591077 | 46 (0.260) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4901392 | 146 (0.620) | 43 (0.210) | 23/252 | 11.9 | 26.4% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4901439 | 115 (0.570) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 5482087 = | 118 (0.500) | 37 (0.220) | 17/212 | 12.1 | 29.6% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5482186 = | 91 (0.530) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 1972137 = | 95 (0.400) | 30 (0.160) | 18/228 | 12.6 | 28.0% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1972233 = | 81 (0.440) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 5518264 | 181 (0.760) | 30 (0.150) | 19/242 | 12.9 | 17.9% | intergenic (+45/‑109) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein |
| ? | NC_002947 | = 5518320 | 127 (0.650) | intergenic (+101/‑53) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947 | 5167567 = | 104 (0.440) | 33 (0.170) | 19/242 | 12.9 | 25.8% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947 | 5167651 = | 104 (0.530) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||