Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	23	39,722	T→G	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	23	39,722	0	T	G	98.7%	267.5 / ‑4.4	78	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (28/48);  total (28/50)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.58e-01

GCAACAATGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTTATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTAAATT  >  23/39625‑39819                                                                                                  |                                                                                                  gCAACAATGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGAtt                                                                                                >  2:1505034/1‑101 (MQ=255)  caacaaTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTg                                                                                               >  1:1546175/1‑101 (MQ=255)  caacaaTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTg                                                                                               >  1:1303962/1‑101 (MQ=255)     caaTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAg                                                                                            <  1:687992/101‑1 (MQ=255)     caaTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAg                                                                                            >  1:1497516/1‑101 (MQ=255)     caaTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAg                                                                                            <  2:895884/101‑1 (MQ=255)       aTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGtt                                                                                          <  2:144216/101‑1 (MQ=255)       aTGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGtt                                                                                          >  1:1385972/1‑101 (MQ=255)        tggcgccgcCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTCATTGGAGttt                                                                                         <  2:1131589/98‑1 (MQ=255)         gACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTTATTGGAGtttt                                                                                        <  1:83450/101‑1 (MQ=255)          aCGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTc                                                                                       <  1:368195/101‑1 (MQ=255)           cgccgcCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCa                                                                                      <  2:1428309/101‑1 (MQ=255)             ccgccgTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAgc                                                                                    <  1:407287/101‑1 (MQ=255)                 cgTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTg                                                                                >  2:978717/1‑101 (MQ=255)                  gTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTgg                                                                               >  2:1448262/1‑101 (MQ=255)                  gTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTgg                                                                               >  2:1120044/1‑101 (MQ=255)                  gTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTgg                                                                               >  1:1178170/1‑101 (MQ=255)                  gTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTgg                                                                               >  1:160559/1‑101 (MQ=255)                  gTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTgg                                                                               >  2:1588589/1‑101 (MQ=255)                   ttATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGt                                                                              >  2:1240829/1‑101 (MQ=255)                   ttATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGt                                                                              <  2:660719/101‑1 (MQ=255)                    tATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTa                                                                             >  1:533052/1‑101 (MQ=255)                     aTCAATTTCACAGGTAGTCGGGTTACCGTGCTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAc                                                                            <  1:960889/101‑1 (MQ=255)                     aTCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAc                                                                            >  1:1487564/1‑101 (MQ=255)                      ataaTTTCACAGGTAGTCGAGTTACCGTTCTGACTCGATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAcc                                                                           <  1:1638679/99‑1 (MQ=255)                        aaTTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAcccc                                                                         >  2:1663507/1‑101 (MQ=255)                        aaTTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAcccc                                                                         <  2:946228/101‑1 (MQ=255)                        aaTTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTAcccc                                                                         >  2:1039547/1‑101 (MQ=255)                          tttCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGt                                                                       >  2:1489997/1‑101 (MQ=255)                           ttCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTg                                                                      >  2:298584/1‑101 (MQ=255)                             cacaGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTggg                                                                    >  2:138901/1‑101 (MQ=255)                                aGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCaa                                                                 >  1:1648019/1‑101 (MQ=255)                                   tAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCt                                                              <  1:612048/101‑1 (MQ=255)                                   tAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCt                                                              <  2:645680/101‑1 (MQ=255)                                     gTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCttt                                                            <  2:341063/101‑1 (MQ=255)                                       cGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAg                                                          <  1:1015225/101‑1 (MQ=255)                                       cGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAg                                                          <  2:286279/101‑1 (MQ=255)                                                gTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGacccaaccc                                                 <  1:1277270/101‑1 (MQ=255)                                                gTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGacccaaccc                                                 <  2:121329/101‑1 (MQ=255)                                                 tACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGacccaaccca                                                <  2:23168/101‑1 (MQ=255)                                                 tACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGacccaaccca                                                >  1:868292/1‑101 (MQ=255)                                                    tGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACccacca                                             >  2:1354202/1‑101 (MQ=255)                                                    tGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACccacca                                             >  1:812871/1‑101 (MQ=255)                                                    tGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACccacca                                             >  2:505802/1‑101 (MQ=255)                                                    tGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACccacca                                             <  2:703944/101‑1 (MQ=255)                                                     gACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAg                                            <  1:681645/101‑1 (MQ=255)                                                          aaTTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGtt                                       <  2:1717804/101‑1 (MQ=255)                                                              ccGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTg                                   <  2:1069788/101‑1 (MQ=255)                                                               cGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGt                                  <  1:612857/101‑1 (MQ=255)                                                                 cAGCGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGGTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTaa                                <  2:1546169/101‑1 (MQ=255)                                                                    cGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACa                             >  2:386744/1‑101 (MQ=255)                                                                    cGGTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACa                             <  1:1448268/101‑1 (MQ=255)                                                                     ggTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACAt                            <  2:569266/101‑1 (MQ=255)                                                                     ggTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACAt                            <  1:829609/101‑1 (MQ=255)                                                                      gTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACAtt                           <  1:775176/101‑1 (MQ=255)                                                                      gTAGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACAtt                           <  1:298584/101‑1 (MQ=255)                                                                        aGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTAc                         <  1:1655843/101‑1 (MQ=255)                                                                        aGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTAc                         <  1:6004/101‑1 (MQ=255)                                                                        aGCTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTAc                         >  2:549613/1‑101 (MQ=255)                                                                          cTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCa                       <  1:1505040/101‑1 (MQ=255)                                                                          cTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCa                       <  1:1680934/101‑1 (MQ=255)                                                                          cTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCa                       <  1:1398338/101‑1 (MQ=255)                                                                          cTGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCa                       <  2:48756/101‑1 (MQ=255)                                                                          atGTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCACCCCACCAGGCGTTCTTGTAAACATTACCa                       <  2:206489/100‑1 (MQ=255)                                                                            gTACGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCAtt                     >  1:288505/1‑101 (MQ=255)                                                                               cGCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGaa                  <  1:138901/101‑1 (MQ=255)                                                                                gCTCGAGCCGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTGCCATTGaaa                 <  2:1389014/101‑1 (MQ=255)                                                                                gCTCGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGAACCAACCCACCAGGCGTTCTTGTAAACATTACCATTGaaa                 <  1:1173959/101‑1 (MQ=255)                                                                                   cGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATa              >  2:1120856/1‑101 (MQ=255)                                                                                   cGAGACGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATa              >  1:1207281/1‑101 (MQ=255)                                                                                     agaCGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAAc            <  2:288505/101‑1 (MQ=255)                                                                                     agaCGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAAc            <  1:1140385/101‑1 (MQ=255)                                                                                        cGCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATg         <  1:1238300/101‑1 (MQ=255)                                                                                         gCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATgg        <  1:1240834/101‑1 (MQ=255)                                                                                         gCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATgg        <  2:1303956/101‑1 (MQ=255)                                                                                         gCCATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATgg        <  1:1663513/101‑1 (MQ=255)                                                                                          ccATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGt       <  1:1436437/101‑1 (MQ=255)                                                                                           cATGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTa      <  1:1377480/101‑1 (MQ=255)                                                                                            aTGGGTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTaa     <  2:1126205/101‑1 (MQ=255)                                                                                              gggTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTAAAt   <  2:1539348/101‑1 (MQ=255)                                                                                               ggTGATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTAAAtt  <  1:1120049/101‑1 (MQ=255)                                                                                                  |                                                                                                  GCAACAATGACGCCGCCGTTATCAATTTCACAGGTAGTCGGGTTACCGTACTGACTCAATTCCGCAGCGGTAGCTGTACGCTCGAGACGCCATGGGTTATTGGAGTTTTCAGCGCTGGTACCCCGTGGGCAATCTTTAGACCCAACCCACCAGGCGTTCTTGTAAACATTACCATTGAAAATAACATGGTAAATT  >  23/39625‑39819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑