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 | 61.0% | 246.5 / inf | 326 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 61.0% | 249.2 / inf | 326 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 61.0% | 255.3 / inf | 326 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 8,770 | 0 | G | C | 56.1% | 125.9 / inf | 385 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 56.1% | 111.8 / inf | 385 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,772 | 0 | A | C | 56.0% | inf / inf | 385 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 45.9% | 144.2 / 240.4 | 159 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 45.5% | 156.5 / 257.8 | 156 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 43.6% | 38.3 / inf | 385 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,938 | 0 | C | . | 39.1% | 771.8 / inf | 325 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 39.0% | 197.2 / inf | 326 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,475 | 0 | G | T | 28.1% | 219.8 / 108.0 | 121 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 27.6% | 212.1 / 97.8 | 123 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,472 | 0 | G | A | 27.4% | 208.6 / 96.2 | 124 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 1,466,201 | 0 | T | C | 23.7% | 164.7 / 39.6 | 77 | pseudogene (810/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 1,466,210 | 0 | G | A | 22.1% | 172.2 / 37.6 | 77 | pseudogene (819/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381292 = | NA (NA) | 16 (0.220) | 12/414 | 4.1 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2765420 = | 121 (1.620) | 4 (0.070) | 4/344 | 6.1 | 4.2% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 86 (1.450) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | = 4542690 | 78 (1.050) | 5 (0.070) | 5/414 | 6.4 | 6.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 76 (1.060) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3640591 | 114 (1.530) | 4 (0.060) | 4/388 | 6.6 | 3.7% | intergenic (+46/‑271) | uspA/dtpB | universal stress global stress response regulator/dipeptide/tripeptide:H(+) symporter DtpB |
| ? | NC_000913 | = 3640569 | 105 (1.570) | intergenic (+24/‑293) | uspA/dtpB | universal stress global stress response regulator/dipeptide/tripeptide:H(+) symporter DtpB | |||||
| * | ? | NC_000913 | = 3620868 | NA (NA) | 4 (0.060) | 4/410 | 6.8 | 4.7% | coding (1677/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621008 | 85 (1.140) | coding (1817/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3355606 | 60 (0.800) | 4 (0.060) | 4/416 | 6.9 | 6.6% | coding (882/4461 nt) | gltB | glutamate synthase subunit GltB |
| ? | NC_000913 | = 3355642 | 56 (0.780) | coding (918/4461 nt) | gltB | glutamate synthase subunit GltB | |||||
| * | ? | NC_000913 | = 1604992 | 93 (1.250) | 4 (0.060) | 4/418 | 6.9 | 4.3% | coding (946/993 nt) | lsrD | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| ? | NC_000913 | = 1605005 | 88 (1.220) | coding (959/993 nt) | lsrD | Autoinducer‑2 ABC transporter membrane subunit LsrD | |||||
| * | ? | NC_000913 | 1430276 = | 40 (0.540) | 4 (0.060) | 4/414 | 6.9 | 6.9% | coding (1228/3363 nt) | stfR | Rac prophage; putative membrane protein |
| ? | NC_000913 | 1430422 = | 69 (0.970) | coding (1374/3363 nt) | stfR | Rac prophage; putative membrane protein | |||||
| * | ? | NC_000913 | = 3601762 | 68 (0.910) | 4 (0.050) | 4/424 | 7.0 | 5.8% | coding (325/1059 nt) | ftsX | cell division protein FtsX |
| ? | NC_000913 | = 3601782 | 63 (0.860) | coding (305/1059 nt) | ftsX | cell division protein FtsX | |||||
| * | ? | NC_000913 | = 2070275 | NA (NA) | 4 (0.050) | 4/426 | 7.0 | NA | intergenic (‑95/‑2) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA |
| ? | NC_000913 | 2996364 = | NA (NA) | noncoding (1328/1331 nt) | IS2 | repeat region | |||||