Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	15	43,228	G→A	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	15	43,228	0	G	A	98.7%	251.5 / ‑4.4	74	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (36/37);  total (37/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.96e-01

AACGCCCAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTGCTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGAATTAATTAT  >  15/43130‑43325                                                                                                   |                                                                                                  aaCGCCCAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTtact                                                                                                 <  2:1495681/101‑1 (MQ=255) aaCGCCCAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTtact                                                                                                 >  1:1707943/1‑101 (MQ=255)     cccAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCa                                                                                             >  2:1623456/1‑101 (MQ=255)       cAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGt                                                                                           >  2:1250058/1‑101 (MQ=255)       cAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGt                                                                                           <  1:1350667/101‑1 (MQ=255)           aGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCAt                                                                                       <  2:510611/101‑1 (MQ=255)             gTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCAttt                                                                                     <  2:1302407/101‑1 (MQ=255)                cgcCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTAcc                                                                                  <  2:1295401/101‑1 (MQ=255)                   cAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAgg                                                                               <  1:907338/101‑1 (MQ=255)                    aaTAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGc                                                                              >  1:943828/1‑101 (MQ=255)                      tAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCtt                                                                            <  2:456737/101‑1 (MQ=255)                      tAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCtt                                                                            >  2:68350/1‑101 (MQ=255)                       aaCAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTg                                                                           <  1:1523238/101‑1 (MQ=255)                         cAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGcc                                                                         >  1:792793/1‑101 (MQ=255)                         cAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGcc                                                                         >  1:1388274/1‑101 (MQ=255)                          aGGGAGCTGTGAAATCCATTCGCCTATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCg                                                                        <  1:1636679/101‑1 (MQ=255)                          aGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCg                                                                        <  2:639306/101‑1 (MQ=255)                          aGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCg                                                                        >  1:1348534/1‑101 (MQ=255)                              aGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAg                                                                    <  2:1374667/101‑1 (MQ=255)                              aGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAg                                                                    >  2:589560/1‑101 (MQ=255)                               gCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAgg                                                                   <  1:1383079/101‑1 (MQ=255)                                 tgtgAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGt                                                                 <  2:1152451/101‑1 (MQ=255)                                  gtgAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTc                                                                >  1:1625103/1‑101 (MQ=255)                                  gtgAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTc                                                                <  2:547729/101‑1 (MQ=255)                                  gtgAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTc                                                                >  1:1083304/1‑101 (MQ=255)                                      aaTCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGAtt                                                            <  1:706073/101‑1 (MQ=255)                                       aTCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGAttt                                                           <  1:1228967/101‑1 (MQ=255)                                       aTCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGAttt                                                           <  1:187694/101‑1 (MQ=255)                                        tCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTa                                                          >  2:189227/1‑101 (MQ=255)                                          cATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTAcc                                                        >  2:356960/1‑101 (MQ=255)                                           aTTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCt                                                       >  2:698782/1‑101 (MQ=255)                                           aTTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCt                                                       >  1:299221/1‑101 (MQ=255)                                              cGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGaa                                                    >  1:526846/1‑101 (MQ=255)                                               gCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAAc                                                   <  2:1087744/101‑1 (MQ=255)                                                ccAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTGCTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAAcc                                                  >  2:1716900/1‑101 (MQ=255)                                                 cAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCa                                                 >  1:242470/1‑101 (MQ=255)                                                  aaTTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCAt                                                >  2:1276353/1‑101 (MQ=255)                                                      cGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATcaca                                            <  2:299221/101‑1 (MQ=255)                                                       gCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACAt                                           <  2:413196/101‑1 (MQ=255)                                                       gCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACAt                                           >  2:593649/1‑101 (MQ=255)                                                       gCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACAt                                           <  2:1610550/101‑1 (MQ=255)                                                         ccGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATcc                                         <  2:1625097/101‑1 (MQ=255)                                                          cGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCt                                        >  1:1133698/1‑101 (MQ=255)                                                          cGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCt                                        >  2:638127/1‑101 (MQ=255)                                                          cGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCt                                        >  1:1293820/1‑101 (MQ=255)                                                           ggACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTa                                       >  1:539795/1‑101 (MQ=255)                                                           ggACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTa                                       >  2:698447/1‑101 (MQ=255)                                                             aCGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACa                                     <  2:1707937/101‑1 (MQ=255)                                                                aTTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATg                                  >  2:1065627/1‑101 (MQ=255)                                                                 ttGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATgg                                 <  1:918737/101‑1 (MQ=255)                                                                  tGCCCGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGc                                <  2:745011/101‑1 (MQ=255)                                                                    cccGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCaa                              <  2:719073/101‑1 (MQ=255)                                                                     ccGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAAt                             >  2:1182540/1‑101 (MQ=255)                                                                      cGAGATAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATa                            >  2:1639507/1‑101 (MQ=255)                                                                       gagaTAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATaa                           <  1:103386/101‑1 (MQ=255)                                                                       gagaTAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATaa                           <  2:1433111/101‑1 (MQ=255)                                                                          aTAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAacac                        <  1:1049682/101‑1 (MQ=255)                                                                          aTAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAacac                        >  2:1274769/1‑101 (MQ=255)                                                                           tAAATGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACg                       <  1:622762/101‑1 (MQ=255)                                                                              aTGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCAc                    >  1:209461/1‑101 (MQ=255)                                                                              aTGTGTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCAc                    <  1:935080/101‑1 (MQ=255)                                                                               tgtgTTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACt                   >  2:392019/1‑101 (MQ=255)                                                                                gtgtTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTg                  >  2:16197/1‑101 (MQ=255)                                                                                 tgtTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTgg                 <  2:1133693/101‑1 (MQ=255)                                                                                 tgtTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTgg                 >  2:1450955/1‑101 (MQ=255)                                                                                 tgtTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTgg                 >  2:1583891/1‑101 (MQ=255)                                                                                  gtTCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGc                <  1:602706/101‑1 (MQ=255)                                                                                   ttCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCg               <  2:588219/101‑1 (MQ=255)                                                                                    tCTGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGt              >  2:226804/1‑101 (MQ=255)                                                                                      tGTTGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTgg            >  1:311878/1‑101 (MQ=255)                                                                                        ttGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGaa          <  1:1513267/101‑1 (MQ=255)                                                                                        ttGGCATTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGaa          >  1:1375927/1‑101 (MQ=255)                                                                                          tgCATTCTTACTGCCAGTTCATTTACCAGGGTTGCCGTGAGGGTCGATTTACCTGAACCATCACCTCCTACAATGGCAATAACACGCACTGGCGTGGaatt        <  1:778898/100‑1 (MQ=255)                                                                                             aTTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGaattaat     <  1:1345756/101‑1 (MQ=255)                                                                                             aTTCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGaattaat     <  1:1065632/101‑1 (MQ=255)                                                                                              ttCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGaattaatt    <  1:1380145/101‑1 (MQ=255)                                                                                               tCTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGAattaatta   <  1:1148982/101‑1 (MQ=255)                                                                                                cTTACTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGAATTAattat  >  1:810743/1‑101 (MQ=255)                                                                                                   |                                                                                                  AACGCCCAAAAGGTGCGCCAATAACAGGGAGCTGTGAAATCCATTCGCCAATTCGCCCGGACGATTGCCCGAGATAAATGTGTTCTGTTGGCATTCTTGCTGCCAGTTCATTTACCAGGCTTGCCGTGAGGGTCGATTTACCTGAACCATCACATCCTACAATGGCAATAACACGCACTGGCGTGGAATTAATTAT  >  15/43130‑43325

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑