| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,315,088 | T→A | 100% | K61I (AAA→ATA) | ndhE ← | NAD(P)H‑quinone oxidoreductase subunit 4L, chloroplastic |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,315,088 | 0 | T | A | 100.0% | 39.9 / NA | 13 | K61I (AAA→ATA) | ndhE | NAD(P)H‑quinone oxidoreductase subunit 4L, chloroplastic |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (6/7); total (6/7) | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
TCCCTCTTAATGTCGCATATATAATAATGACGCTAATTGGAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATTTATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATGATAAGTGGTAAGTACAAACCAATTTAGCCCTATTT > USA300TCH1516_ALE/2314954‑2315211 | tCCCTCTCTGTGTCGCATATATAATAATGTCGCTAATTGGAATGGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAACTGTAATTCTCAGCAATCGCCCTTTATCATATATATCgg < 2:35627/141‑1 (MQ=255) cccTCTTAATGTCGCATATATAATAATGACGCTAATTGGAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGc > 1:82012/1‑141 (MQ=255) ttAATGTCGCATATATAATAATGACGCTAATTGGAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTg > 1:44445/1‑141 (MQ=255) gCTAATTGGAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGtaataa < 2:131389/141‑1 (MQ=255) ggAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGt < 2:104915/141‑1 (MQ=255) aGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATc > 2:99045/1‑141 (MQ=255) caTAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGa < 2:135819/141‑1 (MQ=255) tACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATg > 2:50795/1‑141 (MQ=255) tgaAATTGTAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGATATGATAAGTGGTAAGTAc > 1:117140/1‑141 (MQ=255) tAATTCTCAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATGATAAGTGGTAAGTACAAACCAAt < 2:69829/141‑1 (MQ=255) tcAGCAATCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTAAAAAAAAAAAAAAATTGACAATCCCCAGATAAACTGCGTTATGAAAAGTGGTAAGTACAAACCAATTTAGcc < 2:44445/141‑1 (MQ=255) aTCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATGATAAGTGGTAAGTACAAACCAATTTAGCCCTAttt < 1:39109/141‑1 (MQ=255) aTCGCCCTTTATCATATATATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATGATAAGTGGTAAGTACAAACCAATTTAGCCCTAttt > 2:73140/1‑141 (MQ=255) | TCCCTCTTAATGTCGCATATATAATAATGACGCTAATTGGAATTGCAGTGAAACTATACGTGAGCACACATAAAATTGCAGTTACTAAAAATGATGATGAAATTGTAATTCTCAGCAATCGCCCTTTATCATATTTATCGGCAATTGCCCCTGCCCACACACTTAGTAATAATATTGGTACAAGTCTGCAAAAATTGACAATCCCCAGATAAACTGCGTTATGATAAGTGGTAAGTACAAACCAATTTAGCCCTATTT > USA300TCH1516_ALE/2314954‑2315211 |
| 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: ‑ |