Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	74	15,089	T→G	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	74	15,089	0	T	G	97.1%	236.5 / ‑2.2	69	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (2/0);  new base G (38/29);  total (40/29)
Fisher's exact test for biased strand distribution p-value = 5.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGC  >  74/14991‑15185                                                                                                   |                                                                                                 aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCt                                                                                                <  1:291888/101‑1 (MQ=255)     gTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCAt                                                                                            >  2:1334320/1‑101 (MQ=255)     gTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCAt                                                                                            <  2:356677/101‑1 (MQ=255)     gTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCAt                                                                                            <  1:324683/101‑1 (MQ=255)     gTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAAAGATACGAATGTGCGGGGGCTGCAt                                                                                            >  1:761040/1‑101 (MQ=255)       cGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGt                                                                                          >  1:1696988/1‑101 (MQ=255)        gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGtt                                                                                         >  2:763337/1‑101 (MQ=255)         cTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGttt                                                                                        >  1:1020377/1‑101 (MQ=255)           tCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGc                                                                                      <  1:1610286/101‑1 (MQ=255)            cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCt                                                                                     <  1:291538/101‑1 (MQ=255)             gAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTa                                                                                    >  1:445587/1‑101 (MQ=255)              aaaaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTAc                                                                                   >  2:1353059/1‑101 (MQ=255)               aaaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTAcc                                                                                  >  2:1026732/1‑101 (MQ=255)               aaaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTAcc                                                                                  >  1:1347097/1‑101 (MQ=255)                aaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCt                                                                                 >  2:572270/1‑101 (MQ=255)                      atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTg                                                                           >  2:146129/1‑101 (MQ=255)                           cTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAAc                                                                      <  2:703380/101‑1 (MQ=255)                               cGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTaaa                                                                  <  2:160711/101‑1 (MQ=255)                                  ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCg                                                               >  1:204220/1‑101 (MQ=255)                                  ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCg                                                               >  2:472050/1‑101 (MQ=255)                                    cGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGaa                                                             >  1:1244597/1‑101 (MQ=255)                                    cGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGaa                                                             >  2:801855/1‑101 (MQ=255)                                      aaaaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAAc                                                           >  2:784193/1‑101 (MQ=255)                                      aaaaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAAc                                                           >  1:1436953/1‑101 (MQ=255)                                       aaaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACa                                                          >  1:247448/1‑101 (MQ=255)                                        aaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAg                                                         <  2:1088868/101‑1 (MQ=255)                                        aaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAg                                                         >  1:1597474/1‑101 (MQ=255)                                         aTACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAgg                                                        >  2:476920/1‑101 (MQ=255)                                           aCTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGaa                                                      <  2:107043/101‑1 (MQ=255)                                               ttCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTAc                                                  >  1:220287/1‑101 (MQ=255)                                               ttCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTAc                                                  <  2:1696982/101‑1 (MQ=255)                                               ttCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTAc                                                  <  1:710216/101‑1 (MQ=255)                                                  aaCGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                               >  1:764044/1‑101 (MQ=255)                                                  aaCGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                               <  1:146129/101‑1 (MQ=255)                                                  aaCGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                               <  1:1677806/101‑1 (MQ=255)                                                    cGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAg                                             >  2:1591039/1‑101 (MQ=255)                                                    cGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAg                                             >  2:1394655/1‑101 (MQ=255)                                                      tgtTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTc                                           >  2:576259/1‑101 (MQ=255)                                                       gtTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTcc                                          >  1:173720/1‑101 (MQ=255)                                                        ttGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTccc                                         <  2:1048324/101‑1 (MQ=255)                                                        ttGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTccc                                         >  2:586576/1‑101 (MQ=255)                                                        ttGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTccc                                         <  2:1381846/101‑1 (MQ=255)                                                         tGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCt                                        >  2:1278570/1‑101 (MQ=255)                                                          gCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTg                                       <  2:913701/101‑1 (MQ=255)                                                          gCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTg                                       <  1:522114/101‑1 (MQ=255)                                                             tgtTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcc                                    <  1:605551/101‑1 (MQ=255)                                                              gtTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcct                                   >  1:396020/1‑101 (MQ=255)                                                               ttACCAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcctg                                  >  1:773289/1‑101 (MQ=255)                                                                   cAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcctgcctg                              >  1:893232/1‑101 (MQ=255)                                                                   cAACTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcctgcctg                              >  1:1528234/1‑101 (MQ=255)                                                                    aaCTCGTTTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGa                             >  2:153512/1‑101 (MQ=255)                                                                    aaCTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGa                             >  1:1227498/1‑101 (MQ=255)                                                                     aCTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGat                            <  2:445582/101‑1 (MQ=255)                                                                     aCTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGat                            <  2:1597468/101‑1 (MQ=255)                                                                      cTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatg                           <  1:1353065/101‑1 (MQ=255)                                                                      cTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatg                           <  1:851128/101‑1 (MQ=255)                                                                      cTCGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatg                           <  2:247205/101‑1 (MQ=255)                                                                        cGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatgca                         <  2:204220/101‑1 (MQ=255)                                                                        cGTTTTCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatgca                         >  1:240910/1‑101 (MQ=255)                                                                        cGTATTCAACGATAACAATGTGTGTGGGGTTCATGCTTGCTACCTAAATTGCCAACTAAATCGAAACAGAAAGTACAAAAGCCCATGAcctgcctgccgca                         >  2:255308/1‑96 (MQ=255)                                                                           tttCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGatgcatgc                      <  1:279676/101‑1 (MQ=255)                                                                            ttCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCAtgct                     <  1:295700/101‑1 (MQ=255)                                                                             tCAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCAtgctg                    >  1:881248/1‑101 (MQ=255)                                                                              cAACGATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCAtgctgc                   >  2:1147790/1‑101 (MQ=255)                                                                                  gATAAGAATGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGCCCTGCCTGATGCATGCTGCAAAt               <  2:1020372/101‑1 (MQ=255)                                                                                        aaTGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACAt         >  2:1357353/1‑101 (MQ=255)                                                                                         aTGTGCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATg        >  1:172561/1‑101 (MQ=255)                                                                                          tgtgCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGa       <  2:1464535/101‑1 (MQ=255)                                                                                          tgtgCGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGa       <  1:1199774/101‑1 (MQ=255)                                                                                              cGGGGGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCgg   >  1:405729/1‑101 (MQ=255)                                                                                               ggggGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGc  >  2:894569/1‑101 (MQ=255)                                                                                               ggggGCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGc  >  1:447398/1‑101 (MQ=255)                                                                                                   |                                                                                                 ATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTTTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGC  >  74/14991‑15185

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑