Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	87	3,540	A→T	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	87	3,540	0	A	T	94.7%	251.5 / 4.0	76	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base A (3/1);  new base T (32/40);  total (35/41)
Fisher's exact test for biased strand distribution p-value = 3.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.85e-01

GTTCCGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAATGCGTAAA  >  87/3442‑3636                                                                                                   |                                                                                                 gtTCCGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCg                                                                                                <  1:1695072/101‑1 (MQ=255) gtTCCGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCg                                                                                                >  2:112835/1‑101 (MQ=255)     cGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaa                                                                                            <  2:1576213/101‑1 (MQ=255)     cGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaa                                                                                            >  1:379377/1‑101 (MQ=255)      ggAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaac                                                                                           <  2:1261630/101‑1 (MQ=255)      ggAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaac                                                                                           >  1:1201478/1‑101 (MQ=255)        agaCCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaacaa                                                                                         >  2:1570023/1‑101 (MQ=255)        agaCCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaacaa                                                                                         <  2:1681112/101‑1 (MQ=255)         gaCCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaacaac                                                                                        <  1:214387/101‑1 (MQ=255)         gaCCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGGCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATaacaac                                                                                        <  2:116766/101‑1 (MQ=255)          aCCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAacaaca                                                                                       <  1:583004/101‑1 (MQ=255)            cTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACatt                                                                                     <  1:281946/101‑1 (MQ=255)             tGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACattt                                                                                    <  1:607636/101‑1 (MQ=255)                cggcAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACatttatt                                                                                 >  2:1335078/1‑101 (MQ=255)                  gcAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACAtttattta                                                                               <  1:1013609/101‑1 (MQ=255)                   cAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTaa                                                                              <  2:788261/101‑1 (MQ=255)                   cAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTaa                                                                              <  2:254636/101‑1 (MQ=255)                    aGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAAt                                                                             >  1:352534/1‑101 (MQ=255)                       ataGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAAtttt                                                                          <  1:329104/101‑1 (MQ=255)                        taGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAAttttt                                                                         >  2:1381819/1‑101 (MQ=255)                         aGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTa                                                                        >  2:1036617/1‑101 (MQ=255)                            tCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatc                                                                     <  2:1713563/101‑1 (MQ=255)                             tgTTCACAAAAGCATTACAATTAACCTACATATAGTTTGACGGGTTTTATCCTGAATGGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAagca                                                                    <  2:1068037/100‑1 (MQ=255)                             cGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatca                                                                    <  1:807876/101‑1 (MQ=255)                              gTTCACAAAATCATTACAATTAACCTCCATATAGTTTGTCGGGCTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatcat                                                                   >  1:688301/1‑101 (MQ=255)                              gTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatcat                                                                   <  1:112835/101‑1 (MQ=255)                              gTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatcat                                                                   >  2:523107/1‑101 (MQ=255)                              gTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCAAGGTCTCGATAACAACATTTATTTAATTTTTAatcat                                                                   >  1:1617996/1‑101 (MQ=255)                               ttCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatcatc                                                                  <  1:79485/101‑1 (MQ=255)                               ttCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAatcatc                                                                  <  2:1381380/101‑1 (MQ=255)                                 cacaAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTa                                                                >  2:830448/1‑101 (MQ=255)                                  acaAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTaa                                                               <  2:1157419/101‑1 (MQ=255)                                     aaaTCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTAAttt                                                            >  2:1179610/1‑101 (MQ=255)                                       aTCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGa                                                          >  2:159745/1‑101 (MQ=255)                                          aTTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACaa                                                       >  1:706839/1‑101 (MQ=255)                                          aTTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACaa                                                       >  2:1634290/1‑101 (MQ=255)                                           ttACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAAt                                                      <  2:1202239/101‑1 (MQ=255)                                              cAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTAAATTTTTAATCATCTAATTTGACAATCAt                                                   >  2:231055/1‑101 (MQ=255)                                                aTTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTc                                                 >  2:626140/1‑101 (MQ=255)                                                 ttAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTca                                                <  1:513899/101‑1 (MQ=255)                                                   aaCCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTcaac                                              >  2:180922/1‑101 (MQ=255)                                                     ccTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTcaacaa                                            >  2:123604/1‑101 (MQ=255)                                                      cTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACaaa                                           >  2:1170484/1‑101 (MQ=255)                                                      cTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACaaa                                           >  2:1079040/1‑101 (MQ=255)                                                      cTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACaaa                                           >  1:472059/1‑101 (MQ=255)                                                        aCATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAgt                                         >  2:603737/1‑101 (MQ=255)                                                          atatAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAgttg                                       >  2:40679/1‑101 (MQ=255)                                                              aGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTAc                                   <  1:1657241/101‑1 (MQ=255)                                                              aGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTAc                                   <  1:438058/101‑1 (MQ=255)                                                                tttGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACaa                                 >  2:904996/1‑101 (MQ=255)                                                                tttGTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACaa                                 <  1:1510994/101‑1 (MQ=255)                                                                   gTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACa                              >  1:783090/1‑101 (MQ=255)                                                                   gTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACa                              >  1:334916/1‑101 (MQ=255)                                                                   gTCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACa                              >  1:1187520/1‑101 (MQ=255)                                                                    tCGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACAt                             <  2:1281503/101‑1 (MQ=255)                                                                     cGGGTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACAtt                            <  2:688296/101‑1 (MQ=255)                                                                      gggTTTTATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTa                           <  1:1036622/101‑1 (MQ=255)                                                                         ttttATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCa                        <  1:1634296/101‑1 (MQ=255)                                                                         ttttATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCa                        <  1:682380/101‑1 (MQ=255)                                                                          tttATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAg                       <  1:36172/101‑1 (MQ=255)                                                                           ttATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAgg                      <  2:618075/101‑1 (MQ=255)                                                                            tATCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGa                     >  2:611440/1‑101 (MQ=255)                                                                             aTCCTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGaa                    >  1:507660/1‑101 (MQ=255)                                                                                cTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAg                 >  2:392796/1‑101 (MQ=255)                                                                                cTGAACAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAg                 <  1:109589/101‑1 (MQ=255)                                                                                    aCAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCata             >  2:1560897/1‑101 (MQ=255)                                                                                     cAGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCatat            <  1:1335084/101‑1 (MQ=255)                                                                                      aGTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCAtata           <  1:1079045/101‑1 (MQ=255)                                                                                       gTGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATaa          <  1:392801/101‑1 (MQ=255)                                                                                       gTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATaa          <  1:1179615/101‑1 (MQ=255)                                                                                        tGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAAt         <  2:1188164/101‑1 (MQ=255)                                                                                        tGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAAt         <  2:581419/101‑1 (MQ=255)                                                                                        tGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAAt         <  2:352534/101‑1 (MQ=255)                                                                                        tGATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAAt         <  1:335496/101‑1 (MQ=255)                                                                                         gATCTAGGTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAATg        >  1:476487/1‑101 (MQ=255)                                                                                               ggTCTCGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAATTTGTTACAAACATTACCAGGAAAAGCATATAATGCGTaaa  >  2:1362277/1‑101 (MQ=255)                                                                                                   |                                                                                                 GTTCCGGAGACCTGGCGGCAGTATAGGTCGTTCACAAAATCATTACAATTAACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGTGATCTAGGTCACGATAACAACATTTATTTAATTTTTAATCATCTAATTTGACAATCATTCAACAAAGTTGTTACAAACATTACCAGGAAAAGCATATAATGCGTAAA  >  87/3442‑3636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑