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 | ||
| * | BN000925 | 31,939 | 0 | C | G | 60.8% | 290.3 / inf | 372 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 60.5% | 281.2 / inf | 376 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 60.4% | 279.0 / inf | 376 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 8,772 | 0 | A | C | 54.4% | inf / inf | 462 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 54.3% | 69.4 / inf | 462 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 54.2% | 76.7 / inf | 462 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 45.4% | 328.0 / inf | 339 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 45.2% | inf / inf | 462 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,215 | 0 | A | T | 44.4% | 356.0 / inf | 339 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 31,941 | 1 | . | G | 39.4% | 215.6 / inf | 376 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,938 | 0 | C | . | 39.1% | 876.3 / inf | 368 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,472 | 0 | G | A | 27.8% | 354.5 / 172.7 | 205 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 26.9% | 382.1 / 178.5 | 197 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 26.9% | 355.1 / 161.4 | 197 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 37 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381292 = | NA (NA) | 12 (0.090) | 10/402 | 7.7 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2713829 | 165 (1.230) | 3 (0.040) +79 bp |
3/262 | 8.6 | 2.8% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB |
| ? | NC_000913 | 2713909 = | 170 (1.270) | coding (1014/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB | |||||
| * | ? | NC_000913 | 3817697 = | 132 (0.990) | 7 (0.050) | 6/404 | 9.4 | 5.0% | intergenic (+158/‑63) | yicC/dinD | UPF0701 family protein YicC/DNA damage‑inducible protein D |
| ? | NC_000913 | 3817717 = | 141 (1.100) | intergenic (+178/‑43) | yicC/dinD | UPF0701 family protein YicC/DNA damage‑inducible protein D | |||||
| * | ? | NC_000913 | 1411899 = | 118 (0.880) | 4 (0.030) | 4/368 | 9.9 | 3.2% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 138 (1.180) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||
| * | ? | NC_000913 | = 4542690 | 123 (0.920) | 4 (0.030) | 4/402 | 10.4 | 3.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 130 (1.020) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3617315 = | 123 (0.920) | 4 (0.030) | 4/404 | 10.4 | 3.4% | coding (301/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| ? | NC_000913 | 3617414 = | 112 (0.870) | coding (400/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD | |||||
| * | ? | NC_000913 | = 2962469 | 127 (0.950) | 4 (0.030) | 4/402 | 10.4 | 3.2% | coding (296/324 nt) | ppdC | putative YgdA |
| ? | NC_000913 | = 2962525 | 120 (0.940) | coding (240/324 nt) | ppdC | putative YgdA | |||||
| * | ? | NC_000913 | = 710913 | NA (NA) | 4 (0.030) | 4/400 | 10.4 | NA | noncoding (29/33 nt) | other | REP64 |
| ? | NC_000913 | = 710917 | NA (NA) | noncoding (25/33 nt) | other | REP64 | |||||
| * | ? | NC_000913 | = 4110716 | NA (NA) | 3 (0.020) | 3/402 | 11.0 | NA | noncoding (6/19 nt) | other | REPt303 |
| ? | NC_000913 | = 4110721 | NA (NA) | noncoding (11/19 nt) | other | REPt303 | |||||
| * | ? | NC_000913 | 3927418 = | 129 (0.960) | 6 (0.050) | 3/396 | 11.0 | 4.6% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 130 (1.030) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||