Predicted mutation
evidence seq id position mutation annotation gene description
RA 178 1,308 T→C intergenic (–/–)  /  –/–

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*1781,3080TC97.9% 160.2 / ‑4.1 47intergenic (–/–)–/––/–
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (27/19);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.34e-01

GCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATTCGCTGGTGGATAAAGGACGGTGGACGTGATTG  >  178/1210‑1400
                                                                                                  |                                                                                            
gCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTccc                                                                                            <  1:674870/101‑1 (MQ=255)
gCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTccc                                                                                            <  1:4284/101‑1 (MQ=255)
 cATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCg                                                                                           >  2:1702991/1‑101 (MQ=255)
 cATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCg                                                                                           >  1:645021/1‑101 (MQ=255)
  aTGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGt                                                                                          >  2:95804/1‑101 (MQ=255)
     ggTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGa                                                                                       >  2:313041/1‑101 (MQ=255)
        ggAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGt                                                                                    >  2:1095792/1‑101 (MQ=255)
            cgcAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGGGTTCCGCGTCGACGTTTta                                                                                >  2:603349/1‑101 (MQ=255)
             gcAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTtat                                                                               >  2:528461/1‑101 (MQ=255)
                  attaaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCg                                                                          >  2:274276/4‑101 (MQ=255)
                   ttaaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCgg                                                                         >  1:1589740/3‑101 (MQ=255)
                     aaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCt                                                                       <  2:3315/101‑1 (MQ=255)
                     aaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCt                                                                       >  1:1145009/1‑101 (MQ=255)
                      aaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCtg                                                                      >  2:27810/1‑100 (MQ=255)
                         taccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAAt                                                                   <  1:1687029/99‑1 (MQ=255)
                         taccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAAt                                                                   <  1:527887/99‑1 (MQ=255)
                          tCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATg                                                                  >  1:248130/1‑101 (MQ=255)
                           ccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGc                                                                 >  1:1234652/1‑101 (MQ=255)
                              cTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCgg                                                              >  1:1609158/1‑101 (MQ=255)
                                gACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTg                                                            <  1:1425298/101‑1 (MQ=255)
                                 aCCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGa                                                           <  2:1343210/101‑1 (MQ=255)
                                  ccGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGAt                                                          >  1:1126107/1‑101 (MQ=255)
                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                                                         >  1:227805/1‑101 (MQ=255)
                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                                                         <  1:754377/101‑1 (MQ=255)
                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                                                         >  1:1701181/1‑101 (MQ=255)
                                        cacaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaag                                                    <  2:645016/101‑2 (MQ=255)
                                        cacaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaag                                                    <  1:95804/101‑2 (MQ=255)
                                         acaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaagg                                                   >  1:1433050/1‑99 (MQ=255)
                                            gAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAgggtg                                                >  2:1325789/1‑99 (MQ=255)
                                               aGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCAt                                             <  1:1241588/101‑1 (MQ=255)
                                                gcgggTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTAATCGTAAGGGTGCATg                                            <  1:1492219/98‑1 (MQ=255)
                                                  gggTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCg                                          <  1:313041/100‑1 (MQ=255)
                                                     tataGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAgg                                       <  2:27652/101‑1 (MQ=255)
                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATTGTAAGGGTGCATGCGAGGCGAtt                                  >  1:1435772/1‑101 (MQ=255)
                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGAtt                                  >  2:177155/1‑101 (MQ=255)
                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGAtt                                  >  2:1579656/1‑101 (MQ=255)
                                                                tttGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCtgg                            >  1:1119698/3‑101 (MQ=255)
                                                                 ttGTCCCTATAACATTGGCCCTGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCtggt                           <  2:622556/100‑1 (MQ=255)
                                                                   gTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCtggtgg                         <  1:1439104/101‑1 (MQ=255)
                                                                    tCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGa                        >  2:33228/1‑101 (MQ=255)
                                                                        tataACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATaaa                    <  1:1676492/101‑1 (MQ=255)
                                                                         ataACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATaaaa                   >  1:280073/1‑100 (MQ=255)
                                                                           aaCATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGa                 >  2:570765/1‑101 (MQ=255)
                                                                              aTTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGATgg              >  1:752757/1‑101 (MQ=255)
                                                                              aTTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGATgg              <  2:1525422/101‑1 (MQ=255)
                                                                              aTTGGCCCCGGTAAGNGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGATgg              >  2:414822/1‑101 (MQ=255)
                                                                                  gCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGAtggtggg          <  2:1234647/101‑2 (MQ=255)
                                                                                   ccccGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGAtggtgggc         >  2:1018435/1‑99 (MQ=255)
                                                                                        gTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGATGGTGGGCGCGAt    <  1:274276/101‑1 (MQ=255)
                                                                                         tAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGATAAAAGATGGTGGGCGCGAtt   <  2:1637059/101‑1 (MQ=255)
                                                                                          aattgtTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCAAGCGAGGCGATTCGCTGGTGGATAAAAGATGGTGGGCGCGATTg  <  1:603354/98‑1 (MQ=255)
                                                                                                  |                                                                                            
GCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATTCGCTGGTGGATAAAGGACGGTGGACGTGATTG  >  178/1210‑1400

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: