| 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 | 99.8% | 56.9 / ‑7.4 | 20 | intergenic (+1247/+815) | USA300HOU_1490/USA300HOU_1492 | integrase/possible lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (6/13); minor base G (0/1); total (6/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| 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. | |||||||||||
TCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATT > CP000730/1606997‑1607258 | tCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCCTCCACCTCGAAGGGTATGTTAATCGTCTTGTTTACTTTTTTCCATTTTTAATTGTTGTAt < 2:275301/141‑1 (MQ=255) aTTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCtttt < 1:154965/141‑1 (MQ=255) ttAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTa < 1:40385/141‑1 (MQ=255) tttAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGAc > 2:50508/1‑141 (MQ=255) ttaattaaAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACt > 2:62058/1‑141 (MQ=255) tCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGAtt < 2:105215/141‑1 (MQ=255) cAGAACGTTCAATCGACTCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTAc < 1:265728/141‑1 (MQ=255) aaTCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAt > 2:284703/1‑141 (MQ=255) gAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTACTTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATgtgt < 2:157500/141‑1 (MQ=255) gAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATgtgt < 1:50508/141‑1 (MQ=255) gAATCTCCTGTCCAAACATTTATTGCAATTCGCCCATCCATATCTAATGGTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATgtgt < 1:88090/141‑1 (MQ=255) aaCATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTAttt < 1:168807/141‑1 (MQ=255) aTTGGAATTCGCCCATCCATATCTCATGGTATGTTCATAGTCGTTTTTACTTTTTTCGATTTTTCATTTTTGTATCTTTTACCGTCTGTATTTTGATTAGTGGTTCAGTCTCGTCTGTGTTGTATTTTcacttcagcgtgc > 2:154153/1‑129 (MQ=255) aTTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTcc < 2:161195/141‑1 (MQ=255) cGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTtatacc > 2:269387/1‑139 (MQ=255) atgttatgttAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTAt < 1:243054/141‑1 (MQ=255) tAGTCTTTTTTACTTTTTTCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGCCTGTCCCTTACAGTATCtca > 2:24199/1‑139 (MQ=255) ttCTTTGTTACTTCTCTCCATTTTTATTTTTTGTATCTTCTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATTTGTTATCTTTTCTCTTTAACTTCCTTTTATAACCTCCATGGCTGTCTACTAAAGTATCTAAcc < 2:199182/140‑1 (MQ=255) ttttACTTTTTTTCATTTTTATTTTGTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGc < 1:131483/141‑1 (MQ=255) tCCATTTTTAATTTTTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCAtt < 1:272686/141‑1 (MQ=255) | TCTAAATTAAGTTTAATTAAAGTTCCTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTTAACTTCCTTTTATAACCTACATGGCTGTCTATTAAAGTATCTAACCTGGGCACACCATCATT > CP000730/1606997‑1607258 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |