Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	69	5,269	T→G	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	69	5,269	0	T	G	98.2%	194.1 / ‑4.3	56	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base G (26/29);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 4.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01

CGGAGCCTTCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGATCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGCCAAA  >  69/5174‑5366                                                                                                |                                                                                                  cGGAGCGTTTGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTc                                                                                              <  2:1323111/101‑1 (MQ=255)   gAGCCTTCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCAt                                                                                            >  2:1017208/1‑101 (MQ=255)    aGCCTTCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATc                                                                                           >  1:1369361/1‑101 (MQ=255)     gCCTTCGATTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCt                                                                                          <  1:1626985/101‑1 (MQ=255)       cTTCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGc                                                                                        >  2:333795/1‑101 (MQ=255)         tCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCAc                                                                                      <  2:1563165/101‑1 (MQ=255)          cGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCAcc                                                                                     <  1:1024997/101‑1 (MQ=255)          cGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCAcc                                                                                     <  1:698427/101‑1 (MQ=255)           gACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCa                                                                                    >  1:1408067/1‑101 (MQ=255)                tGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCAc                                                                               <  1:669066/101‑1 (MQ=255)                  ttattaAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGATCCGTCATCTGCACCAGGCACTg                                                                             >  1:1567609/1‑101 (MQ=255)                  ttattaAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTg                                                                             >  2:1340213/1‑101 (MQ=255)                  ttattaAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTg                                                                             >  1:1163038/1‑101 (MQ=255)                  ttattaAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTg                                                                             >  2:912026/1‑101 (MQ=255)                        atccGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCAcc                                                                       <  1:1042619/99‑1 (MQ=255)                         aCCGTTTGATCTCGTAGACTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGCGCACCa                                                                      >  2:1589851/1‑101 (MQ=255)                          ccGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAg                                                                     <  2:1269768/101‑1 (MQ=255)                               tGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGc                                                                >  2:20295/1‑101 (MQ=255)                                gATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCa                                                               <  2:910516/101‑1 (MQ=255)                                  tctcGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAAt                                                             <  1:20295/101‑1 (MQ=255)                                   ctcGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATg                                                            <  2:60096/101‑1 (MQ=255)                                   ctcGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATg                                                            <  2:532489/101‑1 (MQ=255)                                   ctcGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATg                                                            >  2:1330624/1‑101 (MQ=255)                                    tcGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATgg                                                           <  1:751011/101‑1 (MQ=255)                                     cGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATggg                                                          <  1:1401039/101‑1 (MQ=255)                                     cGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATggg                                                          >  1:121042/1‑101 (MQ=255)                                      gATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATgggg                                                         >  2:655793/1‑101 (MQ=255)                                       aTGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATggggg                                                        <  1:985696/101‑1 (MQ=255)                                        tGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGc                                                       <  2:509430/101‑1 (MQ=255)                                        tGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGc                                                       <  2:1369355/101‑1 (MQ=255)                                         gAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATTGGGGca                                                      >  2:1410648/1‑101 (MQ=255)                                         gAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGca                                                      <  1:1428690/101‑1 (MQ=255)                                         gAGTTAAATTTAATCGTTCAGCGCGCTTTACAACTCCAGACAATGAAAAAAAAGAGCCGTCATCTGCACTAGGCACTGAGGACCAGCTGGCAATGGGGGca                                                      >  2:1066582/1‑101 (MQ=255)                                          aGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGcac                                                     >  1:1342080/1‑101 (MQ=255)                                           gTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGAACCAGGCACTGAGCACCAGCTGGCAATGGGGGcaca                                                    >  2:1428617/1‑101 (MQ=255)                                            ttGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACAt                                                   >  2:646550/1‑101 (MQ=255)                                                aTTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATtctc                                               <  1:1020107/101‑1 (MQ=255)                                                 tttAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCa                                              <  2:666744/101‑1 (MQ=255)                                                 tttAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCa                                              <  2:803780/101‑1 (MQ=255)                                                    aaTCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCa                                           >  2:656304/1‑101 (MQ=255)                                                     aTCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCaa                                          >  2:909952/1‑101 (MQ=255)                                                      tCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAAc                                         >  2:362126/1‑101 (MQ=255)                                                      tCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAAc                                         >  1:1324398/1‑101 (MQ=255)                                                        gTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAg                                       >  1:756032/1‑101 (MQ=255)                                                                cgcTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCga                               >  1:360547/1‑101 (MQ=255)                                                                 gcTTTACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCgat                              >  2:1321743/1‑101 (MQ=255)                                                                    ttACACCTCCAGTCACTCAAAAAAGAGAGCCGTCATCTGCACCAGGCCCTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCgatgat                           <  2:39656/101‑1 (MQ=255)                                                                    ttACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCgatgat                           <  1:935373/101‑1 (MQ=255)                                                                    ttACAACTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCgatgat                           <  2:353008/101‑1 (MQ=255)                                                                          cTCCAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACAt                     <  2:420044/101‑1 (MQ=255)                                                                            ccAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCt                   <  2:1163033/101‑1 (MQ=255)                                                                             cAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTg                  <  2:337534/101‑1 (MQ=255)                                                                             cAGTCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTg                  <  1:1620202/101‑1 (MQ=255)                                                                                tCAATGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCaa               >  1:1196831/1‑101 (MQ=255)                                                                                  aaTGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAg             <  1:267993/101‑1 (MQ=255)                                                                                   aTGAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGa            >  2:1147050/1‑101 (MQ=255)                                                                                    agAAAAAAGAGAGCCGTCATCTGCACCAGGCTCTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGac           <  2:505382/100‑1 (MQ=255)                                                                                     gAAAAAAGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCGCCAACAGCCCGGCGATGATGGACATCTGCAAAGaca          <  2:1521585/101‑1 (MQ=255)                                                                                      aaaaaaGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATCGACATCTGCAAAGacac         >  2:1313278/1‑101 (MQ=255)                                                                                       aaaaaGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACAcc        >  1:1475707/1‑101 (MQ=255)                                                                                       aaaaaGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACAcc        <  1:413819/101‑1 (MQ=255)                                                                                         aaaGAGAGCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGc      >  2:55751/1‑101 (MQ=255)                                                                                           agagagCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGCCa    >  2:1550611/1‑101 (MQ=255)                                                                                           agagagCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGCCa    >  2:1608286/1‑101 (MQ=255)                                                                                             agagCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGCCaaa  >  2:687324/1‑101 (MQ=255)                                                                                                |                                                                                                  CGGAGCCTTCGACTATGTTATTAAACCGTTTGATCTCGATGAGTTGAATTTAATCGTTCAGCGCGCTTTACAACTCCAGTCAATGAAAAAAGAGATCCGTCATCTGCACCAGGCACTGAGCACCAGCTGGCAATGGGGGCACATTCTCACCAACAGCCCGGCGATGATGGACATCTGCAAAGACACCGCCAAA  >  69/5174‑5366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑