Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	19	16,992	T→C	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	19	16,992	0	T	C	98.1%	176.9 / ‑4.7	53	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (34/18);  total (34/19)
Fisher's exact test for biased strand distribution p-value = 3.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.89e-01

GAAACAACCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGTGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGTTATCTCTG  >  19/16894‑17088                                                                                                   |                                                                                                 gAAACAACCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGgacagcga                                                                                                >  1:1333116/1‑101 (MQ=255)  aaaCAACCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTGGGATGTCGTATAAGATTAGgacagcgac                                                                                               <  2:1704967/101‑1 (MQ=255)    acaacCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGgacagcgacag                                                                                             >  1:1146235/1‑101 (MQ=255)    acaacCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGgacagcgacag                                                                                             <  2:723173/101‑1 (MQ=255)     caacCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGgacagcgacagt                                                                                            <  2:1404228/101‑1 (MQ=255)     caacCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGgacagcgacagt                                                                                            <  1:1347275/101‑1 (MQ=255)      aacCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTc                                                                                           >  2:1330144/1‑101 (MQ=255)         cAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGtt                                                                                        >  2:509778/1‑101 (MQ=255)          aGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGNTTAGGNCAGCGACAGTCGttt                                                                                       >  2:900844/1‑101 (MQ=255)           ggTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGtttt                                                                                      >  1:683131/1‑101 (MQ=255)           ggTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGtttt                                                                                      >  2:1707048/1‑101 (MQ=255)           ggTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGAGGTCGTATAAGATTAGGGCAGCGACAGTCGtttt                                                                                      <  2:213281/101‑1 (MQ=255)            gtgtTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGttttt                                                                                     >  2:614174/1‑101 (MQ=255)             tgtTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTa                                                                                    <  2:1242176/101‑1 (MQ=255)               ttGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGc                                                                                  >  2:856441/1‑101 (MQ=255)                tGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCg                                                                                 <  2:765007/101‑1 (MQ=255)                tGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCg                                                                                 >  2:531504/1‑101 (MQ=255)                     gAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGt                                                                            >  1:215676/1‑101 (MQ=255)                       aCATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCa                                                                          <  1:1516006/101‑1 (MQ=255)                         aTGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACt                                                                        >  1:1003660/1‑101 (MQ=255)                          tGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACtt                                                                       >  2:80962/1‑101 (MQ=255)                           gAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTa                                                                      <  2:908366/101‑1 (MQ=255)                           gAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTa                                                                      >  1:1146320/1‑101 (MQ=255)                              aTCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAAt                                                                   >  2:1317828/1‑101 (MQ=255)                               tCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAAtt                                                                  <  2:1433388/101‑1 (MQ=255)                                 cGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTaa                                                                <  2:1228135/101‑1 (MQ=255)                                  gAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAg                                                               >  2:1504694/1‑101 (MQ=255)                                    aTGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTa                                                             <  1:956155/101‑1 (MQ=255)                                     tGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTaa                                                            >  2:108191/1‑101 (MQ=255)                                      gAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAAc                                                           <  1:833157/101‑1 (MQ=255)                                         aTAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGc                                                        >  1:461547/1‑101 (MQ=255)                                               ccgcGCTGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCa                                                  <  1:717423/101‑1 (MQ=255)                                                   gATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAAc                                              >  2:1545466/1‑101 (MQ=255)                                                   gATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAAc                                              <  1:106785/101‑1 (MQ=255)                                                     tGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAAcgc                                            <  2:1022990/101‑1 (MQ=255)                                                      ggCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAAcgcg                                           <  1:957821/101‑1 (MQ=255)                                                      ggCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAAcgcg                                           >  2:797327/1‑101 (MQ=255)                                                        cGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGAt                                         >  2:1534166/1‑101 (MQ=255)                                                         gATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGAtt                                        >  1:1233502/1‑101 (MQ=255)                                                         gATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGAtt                                        >  1:1443517/1‑101 (MQ=255)                                                            aaaTTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCt                                     >  1:80857/1‑101 (MQ=255)                                                             aaTTAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCtt                                    >  1:155026/1‑101 (MQ=255)                                                               ttAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCa                                  >  1:1272902/1‑101 (MQ=255)                                                                tAATCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAg                                 >  1:883788/1‑101 (MQ=255)                                                                 aaTCTCATTCGGATGTCGTATAAGATTAGGACAGTGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAgc                                <  1:692863/101‑1 (MQ=255)                                                                 aaTCTCATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAgc                                >  1:9468/1‑101 (MQ=255)                                                                     tcATTCGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCACCGctt                            <  2:1714852/101‑1 (MQ=255)                                                                          cGGATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTg                       <  2:815825/101‑1 (MQ=255)                                                                            gATGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGAc                     >  2:1670675/1‑101 (MQ=255)                                                                             aTGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGAcc                    >  1:860362/1‑101 (MQ=255)                                                                              tGTCGTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGAccc                   >  2:102443/1‑101 (MQ=255)                                                                                  gTATAAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCtt               >  1:85343/1‑101 (MQ=255)                                                                                    ataAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCa             >  1:369033/1‑101 (MQ=255)                                                                                     taAGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCaa            >  2:1179664/1‑101 (MQ=255)                                                                                      aaGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAg           >  1:359011/1‑101 (MQ=255)                                                                                       aGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGt          <  2:1333110/101‑1 (MQ=255)                                                                                       aGATTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGt          >  1:1641688/1‑101 (MQ=255)                                                                                         aTTAGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGTTa        <  2:1233497/101‑1 (MQ=255)                                                                                            aGGACAGCGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGTTAtct     <  1:359175/101‑1 (MQ=255)                                                                                               acagcgacagtCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGTTATCTCTg  <  2:1674762/101‑1 (MQ=255)                                                                                                   |                                                                                                 GAAACAACCAGGTGTTGCTTGAACATGAAATCCGAATGAAATAACGCCGCGATGGCGATAAATTAATCTCATTCGGATGTCGTATAAGATTAGGACAGTGACAGTCGTTTTTAGCGATCGTCACTTAAATTAAGTAACTGCTTATCAAAACGCGATTCCTTCAGCGCTTCTTTGACCCGCTTCAAGTTATCTCTG  >  19/16894‑17088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑