| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 46.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 46.6% | ‑3.0 / 13.3 | 15 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| Reads supporting (aligned to +/- strand): ref base A (6/2); new base G (4/3); total (10/5) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.08e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01 | |||||||||||
GTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT > USA300TCH1516_ALE/111384‑111644 | gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat > 2:57376/1‑136 (MQ=255) aaaaCATAAAAAAGGAAATCGAAGACTTTAAGTTTTTGGCGCAATATAGCAATTTTAGAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTTCCGAGTTATTAGGCTAAATG‑TAAAtgcac > 2:54791/1‑132 (MQ=21) aaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATA‑TCAATTAACTAATgatgat < 2:46175/136‑1 (MQ=255) aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATA‑TCAATTAACTAATGATGATtat < 1:157630/136‑1 (MQ=255) aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATA‑TCAATTAACTAATGATGATtat > 2:32851/1‑136 (MQ=255) tAAGTTTTTTACGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTa < 2:160464/136‑1 (MQ=17) aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTCAAAACTCCAGTCCATAGT‑TTGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgagta > 1:161886/1‑131 (MQ=2) ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGACGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCACCAAATAAAgcgc > 2:111058/1‑136 (MQ=255) tataAAGATGGAGATATATCATATAATACAGAGATGCCAAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAACACAAAAACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt > 1:21012/1‑136 (MQ=17) taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg < 1:144173/136‑1 (MQ=255) aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt > 1:86559/1‑136 (MQ=255) gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTATGTAAAATTTATTTTATATTAATTAATAAAGCGTCGAAGCTGTTGTTGAAAgg < 1:36857/136‑1 (MQ=17) ataATCCAGAGGTGCCGAGTTATTAAACAAAATA‑ACAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt > 1:30676/1‑136 (MQ=14) cGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATAATAATGTAAAACAATTACGTAAAAGATATGACATACCAAGAAATAAAGCGAAGCTCACTTCGTTGCCAGGAACAGGGAATTTAAAAGGCTCATCAGt > 2:56795/1‑136 (MQ=14) ttCAGCTCAATA‑TCAATTAACTAATAATGATTATAATATAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat > 1:22474/1‑136 (MQ=255) | GTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATA‑TCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT > USA300TCH1516_ALE/111384‑111644 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |