Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,236	T→A	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,236	0	T	A	100.0%	135.9 / NA	40	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (16/24);  total (16/24)

TTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATG  >  178/1139‑1336                                                                                                  |                                                                                                     tcataccGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATCTTAAAGTACCa                                                                                                   >  2:1439098/6‑101 (MQ=255)  cataccGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCAc                                                                                                  <  1:1491558/97‑1 (MQ=255)      ccGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGAc                                                                                              <  2:924921/101‑1 (MQ=255)           aaTGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGaac                                                                                         <  1:202164/101‑3 (MQ=255)           aaTGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGaac                                                                                         <  1:896725/101‑3 (MQ=255)                ggcTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAg                                                                                    <  2:604516/99‑1 (MQ=255)                    gttgAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCTCTGACCGAACCACAGAAAg                                                                                <  2:773941/98‑1 (MQ=255)                    gTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAg                                                                                <  1:1463269/101‑1 (MQ=255)                       gAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGcgg                                                                             >  2:660976/1‑99 (MQ=255)                        aaGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCggg                                                                            <  2:306868/101‑1 (MQ=255)                          ggAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTa                                                                          >  2:1687023/1‑101 (MQ=255)                                    gaccAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCAtt                                                                <  2:1079333/99‑1 (MQ=255)                                    gaccAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCAtt                                                                <  1:678517/99‑1 (MQ=255)                                         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                                                  <  2:1122911/100‑1 (MQ=255)                                                  taTTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACa                                                  <  2:940395/100‑1 (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                           >  2:1702991/1‑101 (MQ=255)                                                                         cATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTCCCTATAACATTGGCCCCGGTAAGTGTTTCCCg                           >  1:645021/1‑101 (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)                                                                                                  tCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATg  >  1:248130/1‑101 (MQ=255)                                                                                                  |                                                                                                     TTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCCTATAACATTGGCCCTGGTAAGTGTTTTCCGTCGACGTTTTATAAGCGGCTTAATG  >  178/1139‑1336

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: ‑