Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,092	C→T	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,092	0	C	T	98.6%	244.0 / ‑4.6	73	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (33/39);  total (34/39)
Fisher's exact test for biased strand distribution p-value = 4.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

ACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAGGGGAATCACACCACTGCATACCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCA  >  178/996‑1189                                                                                                 |                                                                                                  aCTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTatat                                                                                               <  1:1411191/101‑1 (MQ=255)  cTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATg                                                                                              <  2:1325529/101‑1 (MQ=255)   tGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATgg                                                                                             <  2:1181018/101‑1 (MQ=255)     aTTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGAc                                                                                           >  2:1241583/1‑101 (MQ=255)        gccgtcGGTGCGCCTGCGACTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCAt                                                                                        <  1:113560/101‑1 (MQ=255)         ccgtcggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATc                                                                                       <  2:540766/95‑1 (MQ=255)          cgtcggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGAGCATCt                                                                                      >  1:773946/6‑101 (MQ=255)          cgtcggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCt                                                                                      <  2:1719668/96‑1 (MQ=255)          cgtcggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCt                                                                                      <  2:899452/96‑1 (MQ=255)             cggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTc                                                                                   >  1:32139/3‑101 (MQ=255)             cggTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTc                                                                                   <  2:221257/99‑1 (MQ=255)                tGCGCCAGCGCCTGATATTCTCGAGCAGTTTCTGTATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtg                                                                                <  1:1631113/101‑3 (MQ=255)                  cgccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggt                                                                              <  1:1446082/99‑2 (MQ=255)                  cgccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggt                                                                              <  1:558763/99‑2 (MQ=255)                   gccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggtg                                                                             <  1:1308888/100‑3 (MQ=255)                    ccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGc                                                                            >  2:1425292/1‑101 (MQ=255)                    ccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGc                                                                            >  1:940400/1‑101 (MQ=255)                    ccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGGAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGc                                                                            >  2:893566/1‑101 (MQ=255)                     cTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGcc                                                                           >  1:1576104/1‑100 (MQ=255)                      tGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGcca                                                                          >  2:239314/1‑99 (MQ=255)                        cgccTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAATGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggttccaca                                                                        >  1:924926/3‑94 (MQ=255)                          ccTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAAt                                                                      >  2:1557330/1‑101 (MQ=255)                            tGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAAtgg                                                                    >  1:1057150/1‑101 (MQ=255)                              ataTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAAtggtg                                                                  >  1:375192/3‑101 (MQ=255)                                aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa                                                                >  1:306868/1‑101 (MQ=255)                                aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa                                                                >  2:260702/1‑101 (MQ=255)                                aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa                                                                >  1:1003558/1‑101 (MQ=255)                                aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa                                                                >  2:1508765/1‑101 (MQ=255)                                aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGCATCTGGACCATCTGCCGTGGTGCCATCATGGTGGa                                                                >  2:553664/1‑101 (MQ=255)                                 ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat                                                               >  1:238827/1‑100 (MQ=255)                                 ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat                                                               <  2:863412/101‑2 (MQ=255)                                 ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat                                                               <  2:1344057/101‑2 (MQ=255)                                  tctcGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGatg                                                              <  1:427833/101‑3 (MQ=255)                                     cGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTa                                                           <  2:1385940/101‑1 (MQ=255)                                      gaccAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTaa                                                          >  2:896720/4‑101 (MQ=255)                                       accAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTaag                                                         <  2:32139/99‑2 (MQ=255)                                       accAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTaag                                                         <  2:779067/99‑2 (MQ=255)                                           gTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGcccg                                                     <  2:1430999/101‑3 (MQ=255)                                            tttCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGt                                                    >  2:345800/1‑101 (MQ=255)                                              tCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGtca                                                  <  2:874989/101‑3 (MQ=255)                                               cTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCAt                                                 >  2:1491552/1‑101 (MQ=255)                                                tGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCAta                                                >  2:115537/1‑100 (MQ=255)                                                 ggATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCAtac                                               <  1:1373759/101‑3 (MQ=255)                                                   aTGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCg                                             <  1:241240/101‑1 (MQ=255)                                                   aTGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCg                                             <  2:855774/101‑1 (MQ=255)                                                        aaaGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAAt                                        <  1:345800/101‑1 (MQ=255)                                                        aaaGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAAt                                        <  1:1196651/101‑1 (MQ=255)                                                          agaaGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGa                                      <  2:1242356/101‑1 (MQ=255)                                                          agaaGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGa                                      <  1:577048/101‑1 (MQ=255)                                                           gaaggtaaccacacaACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGag                                     <  1:1449265/92‑2 (MQ=255)                                                            aaggtaaccacacaACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGagg                                    >  1:27652/9‑99 (MQ=255)                                                             aggtaaccacacaACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGaggc                                   >  2:75768/8‑98 (MQ=255)                                                              ggtaaccacacaACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGaggct                                  <  2:1167194/95‑5 (MQ=255)                                                                taaccacacaACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGt                                >  2:1492213/5‑101 (MQ=255)                                                                      cacaacGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAgg                          <  1:1629750/101‑1 (MQ=255)                                                                      cacaacGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAgg                          >  2:1436920/1‑101 (MQ=255)                                                                       acaacggCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGa                         >  2:1385013/7‑101 (MQ=255)                                                                         aacggCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGaaa                       >  1:323094/5‑101 (MQ=255)                                                                             gCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATg                   <  1:1093363/101‑1 (MQ=255)                                                                             gCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATg                   >  1:110419/1‑101 (MQ=255)                                                                             gCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATg                   <  1:86296/101‑1 (MQ=255)                                                                               aTACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATgcg                 >  2:1676486/1‑101 (MQ=255)                                                                                  ccGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGacc              <  2:1405349/101‑1 (MQ=255)                                                                                   cgcgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCa             >  1:103084/1‑101 (MQ=255)                                                                                     cgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAgg           <  2:891984/101‑1 (MQ=255)                                                                                     cgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAgg           <  1:196779/101‑1 (MQ=255)                                                                                       aTGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGtt         <  2:1057145/101‑1 (MQ=255)                                                                                        tGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTa        >  1:1046513/1‑101 (MQ=255)                                                                                        tGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTa        <  1:773091/101‑1 (MQ=255)                                                                                         ggttCCGGTATCTGGACCATCTGTCGTGGTGCCACAATGGTGGATGGCAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa       >  2:202164/4‑101 (MQ=255)                                                                                         ggttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa       <  1:863838/98‑1 (MQ=255)                                                                                         ggttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa       >  1:1079338/4‑101 (MQ=255)                                                                                          gttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAAc      >  1:1525428/3‑101 (MQ=255)                                                                                              cGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGcta  <  1:1557336/101‑3 (MQ=255)                                                                                                 |                                                                                                  ACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAGGGGAATCACACCACTGCATACCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCA  >  178/996‑1189

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: ‑