Predicted mutation
evidence seq id position mutation annotation gene description
RA 178 1,035 T→C intergenic (–/–)  /  –/–

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*1781,0350TC98.7% 258.2 / ‑4.4 74intergenic (–/–)–/––/–
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (28/45);  total (28/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

CCTGATAAATATCCATGAACGTAAAAATCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAGGGGAATCACACCACTGCATACCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTA  >  178/938‑1132
                                                                                                 |                                                                                                 
ccTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAg                                                                                                <  1:387059/101‑1 (MQ=255)
  tGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGtt                                                                                              <  1:154656/101‑1 (MQ=255)
     tAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCt                                                                                           <  2:1625755/101‑1 (MQ=255)
     tAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCt                                                                                           <  2:1560666/101‑1 (MQ=255)
      aaaTATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTg                                                                                          <  1:998209/101‑1 (MQ=255)
       aaTATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTgg                                                                                         <  2:1059682/101‑1 (MQ=255)
             cATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaa                                                                                   <  2:192131/101‑1 (MQ=255)
             cATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaa                                                                                   <  2:1297011/101‑1 (MQ=255)
              aTGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaa                                                                                  <  2:896212/101‑1 (MQ=255)
               tGAACGCAAAAATCAGATACGGCCTGTCGTCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaaa                                                                                 >  1:874994/1‑101 (MQ=255)
               tGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaaa                                                                                 <  1:434989/101‑1 (MQ=255)
                gAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAag                                                                                <  1:371834/101‑1 (MQ=255)
                gAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAag                                                                                >  2:640000/1‑101 (MQ=255)
                  aCGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGGTTGCCGCCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAagaa                                                                              <  2:820048/101‑2 (MQ=255)
                  aCGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAagaa                                                                              <  2:672587/101‑2 (MQ=255)
                     caaaaaTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAaggt                                                                           <  2:981498/100‑2 (MQ=255)
                     caaaaaTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAaggt                                                                           >  2:1190206/2‑100 (MQ=255)
                     caaaaaTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAaggt                                                                           >  1:1088425/2‑100 (MQ=255)
                      aaaaaTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAaggta                                                                          <  1:79404/101‑3 (MQ=255)
                         aaTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTaacc                                                                       <  1:1398889/101‑3 (MQ=255)
                         aaTCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAGGGGAATc                                                                       <  2:1586210/101‑1 (MQ=255)
                          aTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACca                                                                      <  2:204391/101‑1 (MQ=255)
                          aTCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACca                                                                      <  2:1197176/101‑1 (MQ=255)
                            cAGATACGTCCTCTCGGCTGACGTCCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACcaca                                                                    <  2:245876/101‑1 (MQ=255)
                                tACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCAcacaac                                                                >  1:855779/1‑101 (MQ=255)
                                 acggCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCAcacaacg                                                               <  1:152024/98‑2 (MQ=255)
                                 acggCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCAcacaacg                                                               <  1:1656166/98‑2 (MQ=255)
                                     ccTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCAt                                                           >  1:1668162/1‑101 (MQ=255)
                                     ccTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCAt                                                           <  2:960522/101‑1 (MQ=255)
                                      cTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATa                                                          >  1:1250666/1‑101 (MQ=255)
                                      cTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATa                                                          <  1:1595654/101‑1 (MQ=255)
                                       tGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATAc                                                         <  1:124465/101‑1 (MQ=255)
                                       tGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATAc                                                         <  2:1488230/101‑1 (MQ=255)
                                          cGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACcgc                                                      >  1:891989/1‑101 (MQ=255)
                                             ctgccgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGAt                                                   >  2:527882/6‑101 (MQ=255)
                                             ctgccgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGAt                                                   >  2:1629744/6‑101 (MQ=255)
                                              tgccgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATg                                                  <  2:932766/97‑1 (MQ=255)
                                                ccgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATggt                                                <  2:533685/99‑2 (MQ=255)
                                                 cgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATggtt                                               <  1:640005/100‑3 (MQ=255)
                                                 cgTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATggtt                                               <  2:1567722/100‑3 (MQ=255)
                                                      tGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCggt                                          <  2:1088420/101‑2 (MQ=255)
                                                          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                     <  1:558763/99‑2 (MQ=255)
                                                                           cgccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggt                     <  1:1446082/99‑2 (MQ=255)
                                                                            gccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCgtggtg                    <  1:1308888/100‑3 (MQ=255)
                                                                             ccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGc                   >  1:940400/1‑101 (MQ=255)
                                                                             ccTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGc                   >  2:1425292/1‑101 (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       >  1:1003558/1‑101 (MQ=255)
                                                                                         aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa       >  1:306868/1‑101 (MQ=255)
                                                                                         aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa       >  2:1508765/1‑101 (MQ=255)
                                                                                         aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGa       >  2:260702/1‑101 (MQ=255)
                                                                                         aTTCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGCATCTGGACCATCTGCCGTGGTGCCATCATGGTGGa       >  2:553664/1‑101 (MQ=255)
                                                                                          ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat      >  1:238827/1‑100 (MQ=255)
                                                                                          ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat      <  2:1344057/101‑2 (MQ=255)
                                                                                          ttCTCGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGat      <  2:863412/101‑2 (MQ=255)
                                                                                           tctcGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGatg     <  1:427833/101‑3 (MQ=255)
                                                                                              cGACCAGTTTCTGGATGAAAAAGAAGGTAACCACACAACGGCATACCGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTa  <  2:1385940/101‑1 (MQ=255)
                                                                                                 |                                                                                                 
CCTGATAAATATCCATGAACGTAAAAATCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAGGGGAATCACACCACTGCATACCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTA  >  178/938‑1132

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: