Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	144	20	+TT	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	144	20	1	.	T	100.0%	210.8 / NA	60	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (25/35);  total (25/35)
*	144	20	2	.	T	100.0%	211.6 / NA	60	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (25/35);  total (25/35)

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAATGGGTGCAGTACAACTT‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCAAATT  >  144/1‑119                                                                                                      ||                                                                                                    tgattcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACtt                                                                                                       >  1:1393144‑M1/82‑101 (MQ=255) tgattcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACtt                                                                                                       >  1:1090597‑M1/82‑101 (MQ=255)  gattcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAActtt                                                                                                      <  1:1141114‑M1/21‑2 (MQ=255)  gattcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAActtt                                                                                                      >  2:374721‑M1/81‑100 (MQ=255)  gattcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTT‑‑g                                                                                                    >  1:211017‑M1/81‑101 (MQ=255)     tcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTAcaacttttga                                                                                                   >  1:1025884‑M1/78‑97 (MQ=255)     tcacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTAcaacttttga                                                                                                   <  1:311887‑M1/24‑5 (MQ=255)      cacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTacaacttttgaa                                                                                                  >  1:1574053‑M1/77‑96 (MQ=255)      cacgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTacaacttttgaa                                                                                                  <  2:67262‑M1/25‑6 (MQ=255)       acgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGtacaacttttgaag                                                                                                 >  2:918434‑M1/76‑95 (MQ=255)       acgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGtacaacttttgaag                                                                                                 <  1:81407‑M1/26‑7 (MQ=255)        cgacttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctatcccatttcatcgtccaacaAAATGGGTGCAgtacaacttttgaagc                                                                                                >  1:1717742‑M1/75‑94 (MQ=255)           cttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGa                                                                                             >  2:762206‑M1/72‑101 (MQ=255)            ttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGaa                                                                                            >  2:1247734‑M1/71‑101 (MQ=255)            ttcaaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGaa                                                                                            >  2:670744‑M1/71‑101 (MQ=255)               aaggcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAAccc                                                                                         <  2:417472‑M1/34‑1 (MQ=255)                  gcgcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGtt                                                                                      <  1:1278006‑M1/37‑1 (MQ=255)                    gcttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGtttt                                                                                    >  2:105975‑M1/63‑101 (MQ=255)                     cttttcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGttttt                                                                                   >  2:495303‑M1/62‑101 (MQ=255)                         tcaaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCt                                                                               <  1:111760‑M1/44‑1 (MQ=255)                           aaaagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGc                                                                             >  2:544281‑M1/56‑101 (MQ=255)                             aagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCAt                                                                           >  2:1141109‑M1/54‑101 (MQ=255)                             aagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCAt                                                                           >  1:1657168‑M1/54‑101 (MQ=255)                             aagggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCAt                                                                           >  1:449146‑M1/54‑101 (MQ=255)                              agggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATg                                                                          <  2:1004170‑M1/49‑1 (MQ=255)                                ggtattttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGAc                                                                        <  2:1214981‑M1/51‑1 (MQ=255)                                   attttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCa                                                                     <  2:750352‑M1/54‑1 (MQ=255)                                    ttttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCaa                                                                    <  2:340584‑M1/55‑1 (MQ=255)                                    ttttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCaa                                                                    <  1:1123274‑M1/55‑1 (MQ=255)                                    ttttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCaa                                                                    >  1:1644016‑M1/47‑101 (MQ=255)                                      ttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATc                                                                  <  1:348501‑M1/57‑1 (MQ=255)                                      ttggctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATc                                                                  >  2:526209‑M1/45‑101 (MQ=255)                                         gctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTc                                                               >  2:752190‑M1/42‑101 (MQ=255)                                         gctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGAACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCgtg                                                               <  1:1136370‑M1/60‑2 (MQ=255)                                          ctttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCa                                                              <  1:537846‑M1/61‑1 (MQ=255)                                           tttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCaa                                                             >  2:1491358‑M1/40‑101 (MQ=255)                                           tttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCaa                                                             <  1:1561171‑M1/62‑1 (MQ=255)                                            ttgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCaaa                                                            <  1:1707825‑M1/63‑1 (MQ=255)                                             tgacatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCaaaa                                                           <  1:1586390‑M1/64‑1 (MQ=255)                                               acatattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAAtt                                                         <  2:260713‑M1/66‑1 (MQ=255)                                                 atattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAAttct                                                       <  2:129529‑M1/68‑1 (MQ=255)                                                 atattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAAttct                                                       <  1:706575‑M1/68‑1 (MQ=255)                                                 atattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAAttct                                                       <  1:1608156‑M1/68‑1 (MQ=255)                                                  tattaggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAAttctt                                                      <  1:265244‑M1/69‑1 (MQ=255)                                                     taggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGc                                                   >  2:322804‑M1/30‑101 (MQ=255)                                                     taggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGc                                                   >  2:1200857‑M1/30‑101 (MQ=255)                                                      aggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACTCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGcc                                                  <  1:4459‑M1/73‑1 (MQ=255)                                                       ggggctattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGcca                                                 <  1:1114907‑M1/74‑1 (MQ=255)                                                            tattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGt                                            >  1:755916‑M1/23‑101 (MQ=255)                                                            tattccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGt                                            <  1:110053‑M1/79‑1 (MQ=255)                                                             attccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTc                                           <  2:1071519‑M1/80‑1 (MQ=255)                                                             attccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTc                                           <  1:494039‑M1/80‑1 (MQ=255)                                                             attccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTc                                           <  1:635589‑M1/80‑1 (MQ=255)                                                             attccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTc                                           <  2:593399‑M1/80‑1 (MQ=255)                                                              ttccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCa                                          <  1:993538‑M1/81‑1 (MQ=255)                                                               tccatttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAg                                         >  2:64776‑M1/20‑101 (MQ=255)                                                                  atttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCAc                                      >  2:1608150‑M1/17‑101 (MQ=255)                                                                  atttcatcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTATTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGcat                                      <  1:1689166‑M1/85‑2 (MQ=255)                                                                      catcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGcc                                  <  2:50687‑M1/89‑1 (MQ=255)                                                                       atcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCa                                 <  1:516656‑M1/90‑1 (MQ=255)                                                                       atcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCa                                 >  1:796551‑M1/12‑101 (MQ=255)                                                                        tcgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCAt                                >  2:1069464‑M1/11‑101 (MQ=255)                                                                         cgtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATa                               >  1:260713‑M1/10‑101 (MQ=255)                                                                          gtccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATaa                              <  2:282955‑M1/93‑1 (MQ=255)                                                                           tccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAAc                             >  2:480836‑M1/8‑101 (MQ=255)                                                                            ccaacaAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACt                            <  2:1325004‑M1/95‑1 (MQ=255)                                                                                caAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTc                        >  2:45135‑M1/3‑101 (MQ=255)                                                                                 aAAATGGGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTca                       <  2:223293‑M1/100‑1 (MQ=255)                                                                                       GGTGCAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGc                 <  2:1143427‑M1/101‑1 (MQ=255)                                                                                           CAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCaaaa             <  2:456947‑M1/101‑1 (MQ=255)                                                                                           CAGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCaaaa             <  1:141075‑M1/101‑1 (MQ=255)                                                                                            tacaactttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTa          >  1:1576758/9‑101 (MQ=255)                                                                                            tacaactttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTa          >  2:1299108/9‑101 (MQ=255)                                                                                            AGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAg            >  2:386056‑M1/1‑101 (MQ=255)                                                                                            AGTACAACTTTTGAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAg            >  1:1071524‑M1/1‑101 (MQ=255)                                                                                              caactttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGc        >  1:793799/7‑101 (MQ=255)                                                                                               aactttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGcc       <  1:1144778/96‑1 (MQ=255)                                                                                                 ctttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCaa     >  1:709283/4‑101 (MQ=255)                                                                                                 ctttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCaa     <  2:1707819/98‑1 (MQ=255)                                                                                                 ctttt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCaa     <  1:1207026/98‑1 (MQ=255)                                                                                                  attt‑‑GAAGCTGAACCCGTTTTTTTCTGCAGGGCTCAATCCTGAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCaaa    >  2:248490/3‑101 (MQ=255)                                                                                                    tt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCAAAtt  <  2:51980/101‑1 (MQ=255)                                                                                                    tt‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCAAAtt  <  2:462077/101‑1 (MQ=255)                                                                                                      ||                                                                                                    ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAATGGGTGCAGTACAACTT‑‑GAAGCTGAACCCGTTTTTTTCTGCATGACTCAATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATAACTTGTCACATTGCAAAAGTAGCCAAATT  >  144/1‑119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑