Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_007793613,6870CT72.7% 20.5 / 10.8 33D847D (GAC→GAT) SAUSA300_RS02915serine‑aspartate repeat‑containing protein C
Reads supporting (aligned to +/- strand):  ref base C (8/1);  new base T (24/0);  total (32/1)
Fisher's exact test for biased strand distribution p-value = 2.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

CAGACAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCGGATAGCGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAACGA  >  NC_007793/613605‑613776
                                                                                  |                                                                                         
cagacAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATtcagatagcgactcagactcagatagcgactcagactcagatagcga                                                                          >  1:1059774/1‑100 (MQ=255)
cagacAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATtcagatagcgactcagactcagatagcgactcagactcagatagcga                                                                          >  1:4835605/1‑100 (MQ=255)
cagacAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATtcagatagcgactcagactcagatagcgactcagactcagatagcga                                                                          >  1:3312875/1‑100 (MQ=255)
cagacAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATtcagatagcgactcagactcagatagcgactcagactcagatagcca                                                                          >  1:3392501/1‑98 (MQ=255)
 agacAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATtcagatagcgactcagactcagatagcgactcagactcagatagcgac                                                                         >  1:328034/1‑100 (MQ=255)
            cagactcagacAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCGGa                                                              >  1:5238825/1‑100 (MQ=255)
                accagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACCCAGA‑TCGGaagagc                                                         >  1:4478747/3‑95 (MQ=14)
                 ccagacagcgactcagactcagacagcgactcagactCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGA‑TCGGaagagca                                                        >  1:261691/2‑94 (MQ=14)
                  cagatAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGACAGCGACCCAGA‑TCGGaagagcac                                                       >  1:5347175/1‑93 (MQ=14)
                  cagatAGCGACTCAGACTCGGATAGCGACTCAGACTCGGATAGCGACTCAGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGA‑TCGGaagagcac                                                       >  1:5208188/1‑93 (MQ=11)
                  cagacagcgactcagactcagacagcgactcagactCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGTGACCCAGA‑TCGGaagagcac                                                       >  1:2882640/1‑93 (MQ=11)
                  cagacAGTGATTCAGATTCAGACAGCGACTCAGACTCGGATAGCGACTCAGACTCAGACAGCGATTCAGACTCAGATAGCGACCCAGA‑TCGGaagagcac                                                       >  1:948703/1‑93 (MQ=14)
                  cagacAGTGATTCAGATTCAGACAGCAACTCAGACTCGGATAGCGACTCAGACTCAGACAGCGATTCAGACTCAGATAGCGACTCCGA‑TCGGaagagcac                                                       >  1:413798/1‑93 (MQ=14)
                  cagacAGTGATTCAGATCCAGACAGCGACTCAGATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCGGATAGCga                                                        >  1:4851927/1‑100 (MQ=255)
                  cagacAGTGACTCGGACTCAGACAGTGATTCAGACTCAGATAGCGATTCAGACTCAGATAGCGATTCAGACTCAGACAGTGATTCAGA‑TCGGaagagcac                                                       >  1:3412777/1‑93 (MQ=17)
                  cagacAGTGACTCGGACTCAGACAGGGATTCAGACTCAGATAGCGATTCAGACTCAGATAGCGATTCAGACTCAGACAGCAATTCAGA‑TCGGaagagcac                                                       >  1:2516278/1‑93 (MQ=17)
                  cagacAGCGATTCAGATTCAGACAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGCGATTCAGA‑TCGGaagagcac                                                       >  1:1578798/1‑93 (MQ=17)
                  cagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGA‑TCGGaagagcac                                                       >  1:1411128/1‑93 (MQ=11)
                  cagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGA‑TCGGaagagcac                                                       >  1:4812612/1‑93 (MQ=14)
                  cagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGGGACTCAGA‑TCGGaagagcac                                                       >  1:3972907/1‑93 (MQ=14)
                  cagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGCGACTCAGA‑TCGGaagagcac                                                       >  1:3111460/1‑93 (MQ=14)
                  cagacAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGAGACTCAGA‑TCGGaagagcac                                                       >  1:1240805/1‑93 (MQ=14)
                  cagacAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGAGACAGA‑TCGGaagagcac                                                       >  1:4105676/1‑93 (MQ=11)
                  cagacAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACCCAGA‑TCGGaagagcac                                                       >  1:4890014/1‑93 (MQ=11)
                  cagacAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCAACTCAGA‑TCGGaagagcac                                                       >  1:4260720/1‑93 (MQ=11)
                  cagacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGTGACTCAGA‑TCGGaagagcac                                                       >  1:1960736/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGTGACGCAGA‑TCGGaagagcac                                                       >  1:31404/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGCAACTCAGA‑TCGGaagagcac                                                       >  1:10386/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGAGACTCAGA‑TCGGaagagcac                                                       >  1:3023775/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGAAACACAGA‑TCGGaagagcac                                                       >  1:126450/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCAGA‑TCGGaagagcac                                                       >  1:38970/1‑93 (MQ=14)
                  cagacAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGACAGCAACCCAGA‑TCGGaagagcac                                                       >  1:47982/1‑93 (MQ=14)
                   tgacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGC‑ACTCAGA‑TCGGaagagcacac                                                     >  1:490586/2‑91 (MQ=14)
                   tgacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGAGACTCAGA‑TCGGaagagcaca                                                      >  1:2776441/2‑92 (MQ=14)
                   tgacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGAGACTCAGA‑TCGGaagagcaca                                                      >  1:1650232/2‑92 (MQ=14)
                   agacAGTGACTCGGACTCAGACAGTGATTCAGACTCAGATAGCGATTCAGACTCAGATAGCGATTCAGACTCAGACAGCGACGCAGA‑TCGGaagagcaca                                                      >  1:1888428/1‑92 (MQ=17)
                   agacAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGCG‑CTCAGA‑TCGGaagagcacac                                                     >  1:3610760/1‑91 (MQ=14)
                     acAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGCCTCAGACTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCGGATAGCgattc                                                     <  1:2036695/100‑1 (MQ=255)
                     acAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATTCGGATTCAGACAGTGATTCAGATTCAGACAGCGACCCAGA‑TCGGaagagcacacg                                                    >  1:4274539/1‑90 (MQ=14)
                                                                        cagatagcgactcagactcagatagcgactcagactcGGATAGCGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAACGa  >  1:4674434/1‑100 (MQ=255)
                                                                                  |                                                                                         
CAGACAGCGACTCAGACTCAGACAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCAGATAGCGACTCAGACTCGGATAGCGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAACGA  >  NC_007793/613605‑613776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑