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 | 63.4% | 296.7 / inf | 303 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 62.9% | 299.9 / inf | 306 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 62.7% | 278.7 / inf | 306 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | NC_000913 | 380,012 | 2 | . | G | 58.6% | 55.9 / 41.7 | 29 | intergenic (‑131/+57) | frmR/yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| * | BN000925 | 8,770 | 0 | G | C | 57.8% | 166.0 / inf | 349 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 57.8% | 157.8 / inf | 349 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,772 | 0 | A | C | 57.8% | 757.8 / inf | 349 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 42.4% | 159.7 / 186.0 | 144 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 42.1% | 162.6 / 207.3 | 140 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 41.8% | 116.3 / inf | 349 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,941 | 1 | . | G | 36.9% | 252.0 / inf | 306 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,938 | 0 | C | . | 36.8% | 712.7 / inf | 299 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 1,269,897 | 0 | T | G | 22.7% | 92.1 / 26.8 | 44 | noncoding (40/66 nt) | rdlB | small regulatory antisense RNA RdlB |
| * | NC_000913 | 4,168,475 | 0 | G | T | 21.3% | 282.4 / 82.1 | 122 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 21.3% | 267.8 / 65.8 | 122 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,472 | 0 | G | A | 21.3% | 263.2 / 70.5 | 127 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | BN000925 | 38,390 | 1 | . | G | 20.0% | 981.5 / inf | 385 | pseudogene (47/171 nt) | upf35.8 | probable truncation of theoretical product due to sequence errors |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 70 (1.120) | 12 (0.210) | 12/398 | 3.0 | 16.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 57 (0.980) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 61 (0.980) | 4 (0.070) | 4/412 | 5.7 | 6.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 66 (1.100) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3826385 | 61 (0.980) | 4 (0.070) | 4/410 | 5.7 | 6.9% | coding (1176/2082 nt) | recG | ATP‑dependent DNA helicase RecG |
| ? | NC_000913 | = 3826563 | 49 (0.820) | coding (1354/2082 nt) | recG | ATP‑dependent DNA helicase RecG | |||||
| * | ? | NC_000913 | = 3619291 | 51 (0.820) | 6 (0.100) | 4/408 | 5.7 | 16.6% | coding (100/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3619450 | 12 (0.200) | coding (259/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 2713829 | 54 (0.860) | 4 (0.070) | 4/408 | 5.7 | 7.0% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB |
| ? | NC_000913 | = 2713908 | 55 (0.930) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB | |||||
| * | ? | NC_000913 | = 4373269 | NA (NA) | 4 (0.070) | 4/418 | 5.8 | NA | noncoding (28/34 nt) | other | REP328b |
| ? | NC_000913 | 4374576 = | NA (NA) | noncoding (22/29 nt) | other | REPv329b | |||||
| * | ? | NC_000913 | = 2643100 | 89 (1.420) | 3 (0.050) | 3/402 | 6.1 | 3.4% | intergenic (‑256/+29) | rodZ/rlmN | transmembrane component of cytoskeleton/23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase |
| ? | NC_000913 | = 2643110 | 89 (1.520) | intergenic (‑266/+19) | rodZ/rlmN | transmembrane component of cytoskeleton/23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase | |||||
| * | ? | NC_000913 | = 3022580 | 67 (1.070) | 3 (0.050) | 3/414 | 6.2 | 4.3% | coding (1265/2871 nt) | xdhD | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| ? | NC_000913 | = 3022637 | 68 (1.130) | coding (1322/2871 nt) | xdhD | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit | |||||
| * | ? | NC_000913 | 2325137 = | 60 (0.960) | 3 (0.050) | 3/412 | 6.2 | 5.0% | coding (382/1323 nt) | atoE | short chain fatty acid transporter |
| ? | NC_000913 | 2325279 = | 56 (0.930) | coding (524/1323 nt) | atoE | short chain fatty acid transporter | |||||
| * | ? | BN000925 | = 6854 | 400 (1.160) | 17 (0.050) | 12/410 | 16.3 | 4.4% | noncoding (1363/4949 nt) | transposon:Tn1 | repeat region |
| ? | BN000925 | = 6901 | 351 (1.070) | noncoding (1410/4949 nt) | transposon:Tn1 | repeat region | |||||