mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,946,246 | 0 | G | A | 29.9% | 172.9 / 79.8 | 107 | noncoding (2543/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.6% | 246.1 / 102.9 | 140 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 3,705,984 | 0 | T | G | 22.7% | 390.8 / 121.2 | 155 | intergenic (‑194/+114) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,705,985 | 0 | T | C | 22.6% | 350.9 / 95.3 | 155 | intergenic (‑195/+113) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,781,131 | 0 | T | C | 21.2% | 186.1 / 13.3 | 87 | intergenic (+114/‑84) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,706,048 | 0 | G | T | 20.6% | 413.8 / 80.0 | 145 | intergenic (‑258/+50) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,706,017 | 0 | C | T | 20.1% | 354.6 / 71.9 | 149 | intergenic (‑227/+81) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| Marginal new junction evidence (lowest skew 10 of 1294 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3943635 | NA (NA) | 24 (0.260) | 17/184 | 8.2 | 74.2% | intergenic (+125/‑69) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4037446 | 9 (0.090) | intergenic (+111/‑73) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | 1097357 = | NA (NA) | 19 (0.190) +G |
18/196 | 8.4 | NA | intergenic (+528/+208) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097547 = | NA (NA) | intergenic (+718/+18) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 225685 | 117 (1.170) | 22 (0.230) | 16/186 | 8.7 | 16.7% | intergenic (+110/‑74) | alaV/rrlH | tRNA‑Ala/23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 3943636 | NA (NA) | intergenic (+126/‑68) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | = 16507 | NA (NA) | 18 (0.200) | 13/182 | 9.8 | NA | noncoding (1121/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 16511 | NA (NA) | noncoding (1125/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 225281 | NA (NA) | 25 (0.260) | 13/188 | 10.1 | NA | noncoding (1511/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225293 | NA (NA) | noncoding (1523/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 925850 = | 87 (0.870) | 13 (0.140) | 12/186 | 10.5 | 13.7% | intergenic (+310/+34) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | NC_000913 | 925872 = | NA (NA) | intergenic (+332/+12) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 3984320 | NA (NA) | 5 (0.080) +40 bp |
4/118 | 10.8 | 6.1% | noncoding (101/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4373261 = | 131 (1.310) | noncoding (65/99 nt) | RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 3984320 | NA (NA) | 5 (0.080) +40 bp |
4/118 | 10.8 | NA | noncoding (101/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4317965 = | NA (NA) | noncoding (49/83 nt) | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2835114 = | NA (NA) | 5 (0.080) +40 bp |
4/118 | 10.8 | NA | noncoding (48/82 nt) | REP195 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP195 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 3984320 | NA (NA) | noncoding (101/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1134649 = | 93 (0.930) | 5 (0.080) +40 bp |
4/118 | 10.8 | 8.3% | noncoding (64/98 nt) | RIP100 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP100 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 3984320 | NA (NA) | noncoding (101/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||