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 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 3,174,633 | 0 | A | C | 73.9% | 8.7 / 23.4 | 101 | noncoding (2286/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 3,174,667 | 0 | T | C | 47.9% | ‑3.8 / 48.9 | 124 | noncoding (2252/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 3,177,546 | 0 | A | C | 36.9% | ‑3.1 / 14.9 | 65 | noncoding (1095/1555 nt) | rrnB‑16S | ribosomal RNA‑16S |
| * | BS168_reference_genome | 2,063,773 | 0 | T | A | 35.2% | 257.3 / 251.4 | 235 | pseudogene (391/654 nt) | yobHc | fragment of putative DNA phage repair protein; putative defective prophage 6 |
| * | BS168_reference_genome | 3,174,599 | 0 | A | C | 32.0% | ‑0.6 / 22.1 | 82 | noncoding (2320/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 3,174,618 | 0 | A | C | 31.8% | 1.5 / 15.6 | 92 | noncoding (2301/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 474,620 | 0 | A | C | 31.3% | 413.0 / 36.3 | 199 | intergenic (+395/‑111) | ydaG/amj | putative general stress protein/lipid II flippase |
| * | BS168_reference_genome | 3,174,564 | 0 | A | C | 31.0% | ‑2.0 / 18.2 | 58 | noncoding (2355/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 3,177,579 | 0 | A | C | 29.6% | 1.6 / 10.1 | 72 | noncoding (1062/1555 nt) | rrnB‑16S | ribosomal RNA‑16S |
| * | BS168_reference_genome | 3,588,421 | 0 | T | C | 28.6% | 498.5 / 50.6 | 284 | I314V (ATC→GTC) | hisZ | histidyl‑tRNA synthetase‑like subunit of ATP phophoribosyltransferase |
| * | BS168_reference_genome | 112,638 | 0 | T | C | 28.1% | 505.0 / 39.1 | 274 | intergenic (+140/‑162) | gltX/cysE | glutamyl‑tRNA synthetase/serine O‑acetyltransferase |
| * | BS168_reference_genome | 1,346,705 | 0 | A | G | 26.5% | 490.7 / 50.1 | 258 | intergenic (+27/‑26) | xepA/xhlA | phage PBSX; lytic exoenzyme/phage PBSX; putative enzyme |
| * | BS168_reference_genome | 988,175 | 0 | T | C | 26.2% | 447.7 / 52.7 | 267 | L397P (CTT→CCT) | tcyP | (sodium)‑cystine symporter |
| * | BS168_reference_genome | 1,253,180 | 0 | C | G | 26.0% | 414.3 / 55.0 | 198 | G26G (GGC→GGG) | yjcZ | putative type I toxin |
| * | BS168_reference_genome | 2,004,961 | 0 | T | G | 25.5% | 513.5 / 34.3 | 234 | G95G (GGT→GGG) | ggt | membrane bound gamma‑glutamyltranspeptidase |
| * | BS168_reference_genome | 1,253,156 | 0 | T | G | 24.9% | 513.7 / 54.3 | 220 | G18G (GGT→GGG) | yjcZ | putative type I toxin |
| * | BS168_reference_genome | 2,989,826 | 0 | T | C | 24.8% | 311.9 / 21.4 | 154 | intergenic (‑261/+74) | accD/maeB | acetyl‑CoA carboxylase (carboxyltransferase beta subunit)/NADP‑dependent malic enzyme (conversion of malate into pyruvate, anabolic) |
| * | BS168_reference_genome | 2,625,646 | 0 | A | C | 24.8% | 562.7 / 36.0 | 239 | G89G (GGT→GGG) | dnaJ | co‑factor of molecular chaperone |
| * | BS168_reference_genome | 1,088,257 | 0 | G | C | 24.6% | 238.6 / 19.3 | 203 | A21P (GCC→CCC) | hemY | promiscuous protoporphyrinogen IX and coproporphyrinogen III oxidase |
| * | BS168_reference_genome | 3,174,686 | 0 | G | C | 24.5% | 5.5 / 10.7 | 123 | noncoding (2233/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 9457 = | 262 (0.950) | 1523 (5.760) | 15/286 | 12.4 | 86.9% | coding (2464/2466 nt) | gyrA | DNA gyrase (subunit A) |
| ? | BS168_reference_genome | 3484075 = | 210 (0.790) | coding (1392/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | = 9745 | 227 (0.820) | 23 (0.080) +C |
8/296 | 15.2 | 9.7% | intergenic (+286/‑65) | gyrA/rrnO‑16S | DNA gyrase (subunit A)/ribosomal RNA‑16S |
| ? | BS168_reference_genome | = 3178639 | 203 (0.740) | noncoding (2/1555 nt) | rrnB‑16S | ribosomal RNA‑16S | |||||
| * | ? | BS168_reference_genome | 946697 = | NA (NA) | 241 (0.880) +G |
6/296 | 16.1 | 52.2% | noncoding (2/1555 nt) | rrnD‑16S | ribosomal RNA‑16S |
| ? | BS168_reference_genome | 3178705 = | 222 (0.810) | intergenic (‑65/‑601) | rrnB‑16S/thiT | ribosomal RNA‑16S/thiamin permease | |||||
| * | ? | BS168_reference_genome | = 946631 | 190 (0.690) | 7 (0.030) +C |
6/296 | 16.1 | 3.5% | intergenic (+227/‑65) | ygxA/rrnD‑16S | conserved hypothetical protein/ribosomal RNA‑16S |
| ? | BS168_reference_genome | = 3178639 | 203 (0.740) | noncoding (2/1555 nt) | rrnB‑16S | ribosomal RNA‑16S | |||||
| * | ? | BS168_reference_genome | = 635368 | 277 (1.010) | 13 (0.050) +C |
6/296 | 16.1 | 5.2% | intergenic (+95/‑65) | trnE‑Gly/rrnE‑16S | tRNA‑Gly/ribosomal RNA‑16S |
| ? | BS168_reference_genome | = 3178639 | 203 (0.740) | noncoding (2/1555 nt) | rrnB‑16S | ribosomal RNA‑16S | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 3739 = | 4468 (0.730) | 3 (0.000) | 3/284 | 16.2 | 0.055% | intergenic (+24/‑132) | eryR/ampR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 4067 = | 6710 (1.150) | coding (197/861 nt) | ampR | ||||||
| * | ? | BS168_reference_genome | = 230813 | 335 (1.220) | 4 (0.010) | 4/292 | 17.1 | 1.2% | intergenic (+35/+6) | cypC/ybyB | fatty acid beta‑hydroxylating cytochrome P450/conserved protein of unknown function |
| ? | BS168_reference_genome | 230825 = | 329 (1.220) | coding (255/261 nt) | ybyB | conserved protein of unknown function | |||||
| * | ? | BS168_reference_genome | = 3178639 | 203 (0.740) | 11 (0.040) +G |
4/296 | 17.2 | 5.0% | noncoding (2/1555 nt) | rrnB‑16S | ribosomal RNA‑16S |
| ? | BS168_reference_genome | 3178705 = | 222 (0.810) | intergenic (‑65/‑601) | rrnB‑16S/thiT | ribosomal RNA‑16S/thiamin permease | |||||
| * | ? | BS168_reference_genome | = 202431 | 367 (1.330) | 4 (0.010) | 4/294 | 17.2 | 1.1% | intergenic (+165/+116) | ybbU/alkA | hypothetical protein/DNA‑3‑methyladenine glycosylase; prophage 1 region |
| ? | BS168_reference_genome | = 202589 | 338 (1.240) | coding (870/912 nt) | alkA | DNA‑3‑methyladenine glycosylase; prophage 1 region | |||||
| * | ? | BS168_reference_genome | = 3086835 | 323 (1.170) | 3 (0.010) | 3/280 | 17.5 | 0.91% | coding (462/1497 nt) | ytcQ | putative ABC transporter (binding lipoprotein) |
| ? | BS168_reference_genome | = 3636623 | 350 (1.350) | coding (73/432 nt) | fliW | assembly factor of the flagellum | |||||