| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 2,296,329 | 0 | A | C | 42.1% | 52.8 / 12.0 | 38 | intergenic (‑149/‑66) | inaA/yfaH | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (18/4); new base C (0/16); total (18/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.25e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCGATGAAGTTT > REL606/2296256‑2296403 | cGTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTccacc > 1:830942/1‑76 (MQ=255)cGTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTccacc > 1:917723/1‑76 (MQ=255)cGTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑CCATTTGCAGCNCATAGATTccgcc > 1:193746/1‑76 (MQ=255) gTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTccacca > 2:972726/1‑76 (MQ=255) tATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAg < 2:956419/76‑1 (MQ=255) aTTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGc > 1:1197656/1‑76 (MQ=255) ttAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGcc < 2:177308/76‑1 (MQ=255) tAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGcca < 2:153402/76‑1 (MQ=255) aaTGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGccac > 2:156465/1‑76 (MQ=255) tGAATTTCTTTTGCCACTACTAGCGTGACCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATTCCCCCAGccacta < 2:140472/76‑1 (MQ=255) gAATTTCTTTTGCCCCTACTAGCGTGCCCCCGCTTTTCCCCG‑TCATTTGCGGCGCATAGATTCCCCCAGccactac < 2:1023564/76‑1 (MQ=255) ttCTTTTGCCACTACTAGCGTGACCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATTCCCCCAGccactaccact < 2:136942/76‑1 (MQ=255) cTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTaa > 2:411526/1‑76 (MQ=255) tttGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATa > 2:1115339/1‑76 (MQ=255) tttGCCACTACTAGCGTGACACCGCTTNTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATa > 1:1420784/1‑76 (MQ=255) ttGCCACTACTAGCGTGACCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAg < 2:130830/76‑1 (MQ=255) tGCCACTACTAGCGTGACCCCGCTTTTACCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGt < 2:1037702/76‑1 (MQ=255) tGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGt > 1:869199/1‑76 (MQ=255) tGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGt > 1:869216/1‑76 (MQ=255) cACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTgcg > 1:645607/1‑76 (MQ=255) tactaGCGTGACACCGCTTTTACCCT‑TCATCTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGccc > 1:1300829/1‑76 (MQ=255) ctaGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAg > 1:634579/1‑76 (MQ=255) aGCGTGCCCCCGCTTTTCCCCT‑TCATTGGCACCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTa < 2:1259084/76‑1 (MQ=255) aGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTa > 2:23565/1‑76 (MQ=255) gCGTGCCCCCTCTTTTCCCCT‑TCATTTGCAGCGCATAGATTCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAg < 1:686624/76‑1 (MQ=255) gCGTGCCCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATTCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAg < 1:1149846/76‑1 (MQ=255) gCGTGCCCCCGCTTCTCCCCT‑GCATTTGCAGCGCATAGATCCCCCCAGCCACTTCCACCACTAGTGCGCCCAGTat < 2:209691/76‑2 (MQ=255) cGTGCCCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGa < 2:1033274/76‑1 (MQ=255) cGTGACCCCGCTTTTCCCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGa < 1:57965/76‑1 (MQ=255) cGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGa > 1:1027157/1‑76 (MQ=255) gTGACCCCGTTTTTCCCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGAt < 1:521208/76‑1 (MQ=255) gACCCCGTTTTTCCCCT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATaa < 2:723984/76‑1 (MQ=255) cacCTCTTTTCCCCT‑TCTTTTGCGCCGCATAGATTCCCCCAGCCACTACCACTAATNGTGCGCCCAGTAGATaaaa < 1:1336023/76‑1 (MQ=255) gttttCCCCTATCATTGACAGCGAAGAGTTTCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAAtgtg < 1:380487/75‑1 (MQ=255) ttttACCCT‑TCACTTGCAGCGCATAGATTCCANCAACCACTNCCACTAATAGTGCGCCCAGNAGATAAAATGTGaa > 2:1179121/1‑76 (MQ=255) ttccccT‑TCATTTGCAGCGAATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAAtt < 2:1015669/73‑1 (MQ=255) tccccT‑TCATTTGCAGCGCATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAAttt < 2:913442/74‑1 (MQ=255) cT‑TCATTTGCAGCGCATAGNTTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATc > 1:1328521/1‑76 (MQ=255) tttGCAGCGCATAGATTCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCGGTCg < 2:1405147/76‑1 (MQ=255) gCAGCGCATAGATTCCACCAGCCACTACTACTTATAGTGCGCCCAGTNGACAAAATGTGAATTTAATCAGTCGGAt > 1:130649/1‑76 (MQ=255) gCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGAt > 1:493124/1‑76 (MQ=255) aGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCANTCGGATAc > 1:1251360/1‑76 (MQ=255) gcATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGc > 2:680233/1‑76 (MQ=255) cATAGATCCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCg < 1:1043535/76‑1 (MQ=255) tAGATTCCCCCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCGAt < 1:461251/76‑1 (MQ=255) aGATTCCACCAGCCACTACCACNNATAGTGCGCCNNATAGATAATATGTGTATTTAATCAGTCGGATACAGCGATg < 1:1279225/76‑1 (MQ=255) aGATCCCACCAGCCACTACCGCNNATAGTGCGCCNNATAGATAACATGTGGATTTAATCAGTCGGATACAGCGATg < 1:1279215/76‑1 (MQ=255) ccaccaGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCGATGAAGtt > 1:819934/1‑76 (MQ=255) caccaGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCGATGAAGttt > 2:1244809/1‑76 (MQ=255) | CGTATTAATGAATTTCTTTTGCCACTACTAGCGTGACACCGCTTTTACCCT‑TCATTTGCAGCGCATAGATTCCACCAGCCACTACCACTAATAGTGCGCCCAGTAGATAAAATGTGAATTTAATCAGTCGGATACAGCGATGAAGTTT > REL606/2296256‑2296403 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |