Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,275	C→T	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,275	0	C	T	98.0%	165.2 / ‑4.2	50	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (23/26);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.54e-01

GGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATT  >  178/1179‑1368                                                                                                 |                                                                                              ggTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTc                                                                                           <  1:1385019/101‑1 (MQ=255)   ttAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTccc                                                                                         <  1:1190211/101‑1 (MQ=255)        gctaTTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATaa                                                                                    >  1:1100625/4‑101 (MQ=255)         ctaTTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAAc                                                                                   <  1:1479124/99‑1 (MQ=255)          taTTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACa                                                                                  <  2:940395/100‑1 (MQ=255)          taTTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACa                                                                                  <  2:1122911/100‑1 (MQ=255)             tGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTg                                                                               <  2:843630/101‑1 (MQ=255)             tGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTg                                                                               <  2:103084/101‑1 (MQ=255)              gaacgtgATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTgg                                                                              <  2:1046508/95‑1 (MQ=255)                     aTAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGt                                                                       >  1:1637065/1‑101 (MQ=255)                       aaGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTaa                                                                     >  1:1032600/1‑101 (MQ=255)                           cgcTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAgtgt                                                                 <  2:1668156/101‑1 (MQ=255)                            gcTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGtt                                                                <  1:1542695/101‑1 (MQ=255)                             cTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGttt                                                               <  1:115537/101‑1 (MQ=255)                             cTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGttt                                                               <  1:75768/101‑1 (MQ=255)                                gCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTccc                                                            <  1:4284/101‑1 (MQ=255)                                gCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTccc                                                            <  1:674870/101‑1 (MQ=255)                                 cATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCg                                                           >  1:645021/1‑101 (MQ=255)                                 cATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCg                                                           >  2:1702991/1‑101 (MQ=255)                                  aTGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGt                                                          >  2:95804/1‑101 (MQ=255)                                     ggTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGa                                                       >  2:313041/1‑101 (MQ=255)                                        ggAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGt                                                    >  2:1095792/1‑101 (MQ=255)                                            cgcAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGGGTTCCGCGTCGACGTTTta                                                >  2:603349/1‑101 (MQ=255)                                             gcAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTtat                                               >  2:528461/1‑101 (MQ=255)                                                  attaaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCg                                          >  2:274276/4‑101 (MQ=255)                                                   ttaaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCgg                                         >  1:1589740/3‑101 (MQ=255)                                                     aaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCt                                       <  2:3315/101‑1 (MQ=255)                                                     aaaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCt                                       >  1:1145009/1‑101 (MQ=255)                                                      aaGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCtg                                      >  2:27810/1‑100 (MQ=255)                                                         taccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAAt                                   <  1:1687029/99‑1 (MQ=255)                                                         taccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAAt                                   <  1:527887/99‑1 (MQ=255)                                                          tCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATg                                  >  1:248130/1‑101 (MQ=255)                                                           ccACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGc                                 >  1:1234652/1‑101 (MQ=255)                                                              cTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCgg                              >  1:1609158/1‑101 (MQ=255)                                                                gACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTg                            <  1:1425298/101‑1 (MQ=255)                                                                 aCCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGa                           <  2:1343210/101‑1 (MQ=255)                                                                  ccGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGAt                          >  1:1126107/1‑101 (MQ=255)                                                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                         >  1:1701181/1‑101 (MQ=255)                                                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                         <  1:754377/101‑1 (MQ=255)                                                                   cGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATc                         >  1:227805/1‑101 (MQ=255)                                                                        cacaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaag                    <  2:645016/101‑2 (MQ=255)                                                                        cacaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaag                    <  1:95804/101‑2 (MQ=255)                                                                         acaGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTaagg                   >  1:1433050/1‑99 (MQ=255)                                                                            gAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAgggtg                >  2:1325789/1‑99 (MQ=255)                                                                               aGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCAt             <  1:1241588/101‑1 (MQ=255)                                                                                gcgggTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTAATCGTAAGGGTGCATg            <  1:1492219/98‑1 (MQ=255)                                                                                  gggTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCg          <  1:313041/100‑1 (MQ=255)                                                                                     tataGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAgg       <  2:27652/101‑1 (MQ=255)                                                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATTGTAAGGGTGCATGCGAGGCGAtt  >  1:1435772/1‑101 (MQ=255)                                                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGAtt  >  2:177155/1‑101 (MQ=255)                                                                                          cgTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCGTCGACGTTTTATAAGCGGCTGAATGCCGGTGATCGTAAGGGTGCATGCGAGGCGAtt  >  2:1579656/1‑101 (MQ=255)                                                                                                 |                                                                                              GGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATGCCGGTGATCGTAAAGGCGCATGCGAGGCGATT  >  178/1179‑1368

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑