| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000730 | 1,607,132 | C→T | 100% | intergenic (+1247/+815) | USA300HOU_1490 → / ← USA300HOU_1492 | integrase/possible lipoprotein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,607,132 | 0 | C | T | 100.0% | 40.0 / NA | 12 | intergenic (+1247/+815) | USA300HOU_1490/USA300HOU_1492 | integrase/possible lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (2/10); total (2/10) | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. | |||||||||||
AAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGT > CP000730/1607000‑1607263 | aaaTTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCtt > 2:135013/1‑141 (MQ=255) aGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCg < 2:79509/141‑1 (MQ=255) ttaattaaAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACt < 2:40051/141‑1 (MQ=255) tCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGt < 2:18174/141‑1 (MQ=255) cAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTGTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTTATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTAt < 1:100416/141‑1 (MQ=255) ttATTGGAATTCGCCCATCTATATCTAATATTATGTTAATGGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGCTACTGTCTCGTATGTGTTAGCTTTTCTATTTAACtt < 2:41423/141‑1 (MQ=255) ttGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGCTTAGTGGTACAGTATCGTATGTGTTTCCTTTTCTATTTTACTCCCt > 1:51868/1‑141 (MQ=255) ccatccatATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTCTTATAACCTa < 1:3407/141‑1 (MQ=255) catccatATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTAc < 1:46010/141‑1 (MQ=255) tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCAtt < 1:74413/141‑1 (MQ=255) tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCAtt < 1:63539/141‑1 (MQ=255) ttttAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGt < 2:31010/141‑1 (MQ=255) | AAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATTAATGT > CP000730/1607000‑1607263 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |