Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,386	C→T	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,386	0	C	T	100.0%	155.3 / NA	45	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/25);  total (20/25)

ATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATTCGCTGGTGGAT‑AAAGGACGGTGGACGTGATTGCCGCATTCGTTCAAATAATTGTTACGGTCAGGTTATTCGTCGTGACCAGGAGAGTGCATTAACCTGCTGGGGGATAGAAC  >  178/1288‑1480                                                                                                    |                                                                                               aTTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATgg                                                                                              >  1:752757/1‑101 (MQ=255) aTTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATgg                                                                                              <  2:1525422/101‑1 (MQ=255) aTTGGCCCCGGTAAGNGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATgg                                                                                              >  2:414822/1‑101 (MQ=255)     gCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGAtggtggg                                                                                          <  2:1234647/101‑2 (MQ=255)      ccccGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGAtggtgggc                                                                                         >  2:1018435/1‑99 (MQ=255)           gTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGAt                                                                                    <  1:274276/101‑1 (MQ=255)            tAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGAtt                                                                                   <  2:1637059/101‑1 (MQ=255)             aattgtTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCAAGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTg                                                                                  <  1:603354/98‑1 (MQ=255)                     cccGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCAtac                                                                          <  2:1433044/100‑3 (MQ=255)                      ccGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACg                                                                         >  1:359684/1‑101 (MQ=255)                        gTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGtt                                                                       >  2:81095/1‑101 (MQ=255)                        gTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGtt                                                                       >  1:1360889/1‑101 (MQ=255)                         tCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTc                                                                      <  1:1095797/101‑1 (MQ=255)                             cGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAaat                                                                  <  2:238827/101‑1 (MQ=255)                              gTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAaata                                                                 >  1:1209762/1‑101 (MQ=255)                              gTTTTATAAGCGGCTGAATGCCGGGGGTCGTAAGGGTGGATGCGAGGGGATGCGCTGGTGGGT‑TAAAGATGGAGGGAGGGATTGCGGCATACATTCAaata                                                                 >  1:1143699/1‑101 (MQ=255)                                tttATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAaataac                                                               <  1:27810/101‑2 (MQ=255)                                 ttATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAaataact                                                              <  1:1325795/101‑3 (MQ=255)                                  tataAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTg                                                             <  2:110419/101‑1 (MQ=255)                                       gCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTatg                                                        >  2:892557/1‑99 (MQ=255)                                        cGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATgg                                                       >  1:1451271/1‑101 (MQ=255)                                         ggCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATgga                                                      <  2:1119693/101‑2 (MQ=255)                                         ggCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATgga                                                      <  2:1576098/101‑2 (MQ=255)                                          gCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATggac                                                     <  1:1702997/101‑3 (MQ=255)                                           ctgaaTGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACa                                                    <  2:1126102/98‑1 (MQ=255)                                            tgaaTGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAg                                                   >  2:963025/3‑101 (MQ=255)                                            tgaaTGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGAGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAg                                                   >  2:11726/3‑101 (MQ=255)                                               aTGCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGtt                                                >  2:311794/1‑101 (MQ=255)                                                 gCCGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTAt                                              <  2:227805/101‑1 (MQ=255)                                                   cGGTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATtc                                            <  2:1145004/101‑1 (MQ=255)                                                    ggTGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATtcg                                           <  1:879083/101‑1 (MQ=255)                                                      tGATCGTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATtcgtc                                         >  2:221854/1‑101 (MQ=255)                                                           gTAAGGGTGCATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATCCATTCAAATAACTGCTACGGACAGGTTATTCGTCGTGAc                                    <  2:1143694/101‑1 (MQ=255)                                                             aagggtgcATGCGAGCCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCa                                  >  1:209122/7‑101 (MQ=255)                                                              agggtgcATGCGAGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAg                                 <  1:177155/96‑1 (MQ=255)                                                                     aTGCGAGGCGATTCGTTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGaaagcg                          >  2:1466239/1‑99 (MQ=255)                                                                        cGAGGCGATTCGTTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCAt                       <  1:1466245/101‑1 (MQ=255)                                                                          aGGCGATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTa                     <  2:1589734/101‑1 (MQ=255)                                                                              gATTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCct                 >  1:272032/1‑101 (MQ=255)                                                                               aTTCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCctg                >  1:494602/1‑101 (MQ=255)                                                                                ttCGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCctgt               >  2:1495759/1‑100 (MQ=255)                                                                                  cGCTGGTGGAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCctgttg             <  1:528466/101‑1 (MQ=255)                                                                                    cTGGTGGATAAAAGGTTGGTGG‑CGCGCTTTCCGCATACGTTCAAATAACTGGTATGGGCAGGTTTTTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTggg           <  1:414827/101‑1 (MQ=255)                                                                                     tggtggAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTgggg          >  2:605165/1‑101 (MQ=255)                                                                                       gtggAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGa        >  1:41328/1‑101 (MQ=255)                                                                                        tggAT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGAt       <  2:1701175/101‑1 (MQ=255)                                                                                           aT‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGATAGa    >  1:1328072/1‑101 (MQ=255)                                                                                            t‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGATAGat   <  2:1209757/101‑2 (MQ=255)                                                                                            t‑AAAAGATGGTGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGATAGat   <  1:81095/101‑2 (MQ=255)                                                                                              aaaaGATGGGGGGCGCGATTGCCGCATACGTTCAAATAACTGCTATGGACAGGTTATTCGTCGTGACCAGGAAAGCGCATTAGCCTGTTGGGGGATAGatc  >  2:247443/1‑99 (MQ=255)                                                                                                    |                                                                                               ATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATTCGCTGGTGGAT‑AAAGGACGGTGGACGTGATTGCCGCATTCGTTCAAATAATTGTTACGGTCAGGTTATTCGTCGTGACCAGGAGAGTGCATTAACCTGCTGGGGGATAGAAC  >  178/1288‑1480

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: ‑