mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 64.9% | 364.3 / inf | 342 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 64.7% | 377.4 / inf | 343 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 64.7% | 373.5 / inf | 343 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 8,772 | 0 | A | C | 60.4% | 893.1 / inf | 390 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 60.3% | 274.5 / inf | 390 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 60.2% | 271.4 / inf | 390 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 44.9% | 262.5 / inf | 265 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 43.5% | 283.8 / inf | 262 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 39.3% | 209.6 / inf | 390 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,938 | 0 | C | . | 34.7% | 857.5 / inf | 340 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 34.7% | 362.7 / inf | 343 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,296,268 | 0 | T | C | 28.6% | 29.3 / 13.3 | 21 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,168,472 | 0 | G | A | 27.7% | 260.6 / 133.8 | 156 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 26.3% | 318.3 / 130.2 | 152 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 26.1% | 293.2 / 117.4 | 153 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381292 = | NA (NA) | 16 (0.170) | 11/404 | 5.8 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 93 (0.950) | 7 (0.070) | 7/404 | 7.2 | 6.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 108 (1.150) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1198462 = | 145 (1.480) | 4 (0.050) | 4/334 | 7.7 | 3.1% | intergenic (‑225/‑233) | ymfE/lit | e14 prophage; uncharacterized protein YmfE/e14 prophage; cell death peptidase Lit |
| ? | NC_000913 | = 1198453 | 136 (1.760) | intergenic (‑216/‑242) | ymfE/lit | e14 prophage; uncharacterized protein YmfE/e14 prophage; cell death peptidase Lit | |||||
| * | ? | NC_000913 | 447217 = | 160 (1.640) | 5 (0.050) | 4/400 | 8.6 | 3.3% | coding (489/891 nt) | cyoE | heme O synthase |
| ? | NC_000913 | 447278 = | 143 (1.540) | coding (428/891 nt) | cyoE | heme O synthase | |||||
| * | ? | NC_000913 | 2125678 = | 84 (0.860) | 4 (0.040) | 4/406 | 8.7 | 4.7% | coding (69/1224 nt) | wcaI | putative colanic biosynthesis glycosyl transferase |
| ? | NC_000913 | 2125718 = | 82 (0.870) | coding (29/1224 nt) | wcaI | putative colanic biosynthesis glycosyl transferase | |||||
| * | ? | NC_000913 | 1323539 = | 133 (1.360) | 4 (0.040) | 4/404 | 8.7 | 3.2% | coding (320/882 nt) | yciV | RNA/ssDNA 5'‑>3' exonuclease |
| ? | NC_000913 | 1323564 = | 115 (1.230) | coding (345/882 nt) | yciV | RNA/ssDNA 5'‑>3' exonuclease | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 4 (0.040) | 4/408 | 8.7 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3617315 = | 110 (1.130) | 3 (0.030) | 3/406 | 9.3 | 2.9% | coding (301/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| ? | NC_000913 | 3617414 = | 93 (0.990) | coding (400/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD | |||||
| * | ? | NC_000913 | 943655 = | 95 (0.970) | 3 (0.030) | 3/406 | 9.3 | 3.6% | coding (242/618 nt) | dmsB | dimethyl sulfoxide reductase subunit B |
| ? | NC_000913 | 943757 = | 71 (0.750) | coding (344/618 nt) | dmsB | dimethyl sulfoxide reductase subunit B | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 3 (0.030) | 3/404 | 9.3 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||