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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,182,923 | 0 | C | T | 56.4% | 35.1 / 131.9 | 113 | P560L (CCA→CTA) | rpoB | RNA polymerase, beta subunit |
| * | NC_000913 | 4,183,214 | 0 | C | T | 42.9% | 68.2 / 161.0 | 140 | T657I (ACC→ATC) | rpoB | RNA polymerase, beta subunit |
| * | NC_000913 | 4,037,225 | 0 | A | C | 33.3% | 15.2 / 11.7 | 21 | intergenic (+8/‑35) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913 | 4,037,226 | 0 | C | G | 33.3% | 22.8 / 12.2 | 21 | intergenic (+9/‑34) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.1% | 102.9 / 67.7 | 93 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,208,231 | 0 | T | A | 31.0% | 32.0 / 17.5 | 29 | noncoding (85/1542 nt) | rrsE | 16S ribosomal RNA of rrnE operon |
| * | NC_000913 | 4,208,230 | 0 | T | A | 27.6% | 32.5 / 16.8 | 29 | noncoding (84/1542 nt) | rrsE | 16S ribosomal RNA of rrnE operon |
| * | NC_000913 | 223,854 | 0 | T | A | 25.0% | 38.5 / 14.3 | 32 | noncoding (84/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| * | NC_000913 | 223,855 | 0 | T | A | 25.0% | 40.1 / 14.9 | 32 | noncoding (85/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| Marginal new junction evidence (lowest skew 10 of 238 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 33 (0.310) | 37 (0.390) | 28/262 | 3.3 | 47.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 54 (0.570) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3584198 | NA (NA) | 16 (0.250) +59 bp |
10/176 | 5.4 | 17.3% | pseudogene (3/114 nt) | yrhA | pseudogene, interrupted by IS1E |
| ? | NC_000913 | = 4519325 | 128 (1.210) | intergenic (+101/+13) | insB1/yjhU | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 35 (0.350) | 18/280 | 5.8 | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 24 (0.240) | 17/280 | 6.0 | 25.1% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4037457 | 75 (0.710) | intergenic (+122/‑62) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 4168373 | 73 (0.690) | 10 (0.170) +66 bp |
5/162 | 7.2 | 14.3% | noncoding (2/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | = 4209753 | 144 (1.360) | intergenic (+65/‑21) | rrsE/gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 2729443 = | 63 (0.590) | 10 (0.170) +66 bp |
5/162 | 7.2 | 14.9% | noncoding (2/76 nt) | gltW | tRNA‑Glu |
| ? | NC_000913 | = 4209753 | 144 (1.360) | intergenic (+65/‑21) | rrsE/gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 20 (0.200) | 13/280 | 7.3 | 31.3% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 3943642 | 46 (0.430) | intergenic (+132/‑62) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | 2775492 = | 133 (1.250) | 14 (0.140) | 12/274 | 7.5 | 10.7% | intergenic (+471/‑53) | yfjW/ypjI | CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related |
| ? | NC_000913 | 2775516 = | 109 (1.100) | intergenic (+495/‑29) | yfjW/ypjI | CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3665737 = | 127 (1.200) | 12 (0.120) | 11/280 | 8.0 | 9.1% | coding (74/825 nt) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| ? | NC_000913 | 3665756 = | 119 (1.180) | coding (55/825 nt) | gadX | acid resistance regulon transcriptional activator; autoactivator | |||||
| * | ? | NC_000913 | 3083831 = | 123 (1.160) | 18 (0.180) | 10/276 | 8.3 | 13.7% | intergenic (‑34/+104) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding |
| ? | NC_000913 | 3083868 = | 112 (1.130) | intergenic (‑71/+67) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding | |||||