Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,188	C→T	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,188	0	C	T	100.0%	132.6 / NA	39	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/25);  total (14/25)

GGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCC  >  178/1090‑1281                                                                                                   |                                                                                              ggtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAt                                                                                             <  2:1302635/98‑1 (MQ=255)  gtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAtt                                                                                            >  1:830573/3‑101 (MQ=255)  gtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAtt                                                                                            >  2:1479118/3‑101 (MQ=255)     tatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaa                                                                                         <  2:630295/101‑2 (MQ=255)     tatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaa                                                                                         <  2:754573/101‑2 (MQ=255)      atGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaac                                                                                        <  2:1250661/101‑3 (MQ=255)         gACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACgtg                                                                                     >  2:678512/1‑99 (MQ=255)            cATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATa                                                                                  >  1:1343216/1‑101 (MQ=255)            cATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATa                                                                                  <  1:456782/101‑1 (MQ=255)             aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                                 >  2:308636/1‑101 (MQ=255)             aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                                 <  1:438007/101‑1 (MQ=255)             aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                                 >  2:1451688/1‑101 (MQ=255)             aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                                 <  2:1666489/101‑1 (MQ=255)             aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                                 >  1:3315/1‑101 (MQ=255)                         gccacaaTGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATg                                                                     <  1:1508771/95‑1 (MQ=255)                          ccacaaTGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATgg                                                                    >  2:33263/6‑101 (MQ=255)                            acaaTGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGt                                                                  <  2:631206/98‑1 (MQ=255)                              aaTGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTgg                                                                <  2:830568/100‑1 (MQ=255)                                  gtggATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAgcg                                                            <  2:323094/101‑1 (MQ=255)                                   tggATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAgcgc                                                           >  1:939818/1‑101 (MQ=255)                                   tggATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAgcgc                                                           >  2:1283315/1‑101 (MQ=255)                                       tggTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAata                                                       >  1:843635/2‑101 (MQ=255)                                        ggTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGAAatat                                                      <  2:375192/101‑1 (MQ=255)                                             gcccgtcataccGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAg                                                 <  1:308636/91‑1 (MQ=255)                                                cgtcataccGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGtac                                              <  1:1436926/94‑3 (MQ=255)                                                  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         <  1:678517/99‑1 (MQ=255)                                                                                     gaccAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCAtt         <  2:1079333/99‑1 (MQ=255)                                                                                          ggTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTc    <  1:1385019/101‑1 (MQ=255)                                                                                            ttAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGAACCACAGAAAGCGGGTATAGCGTCATTTTGTccc  <  1:1190211/101‑1 (MQ=255)                                                                                                   |                                                                                              GGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTATCGCGTCATTCTGTCCC  >  178/1090‑1281

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: ‑