Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	1,175	C→A	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	1,175	0	C	A	100.0%	159.1 / NA	46	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (19/27);  total (19/27)

CCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTA  >  178/1077‑1264                                                                                                   |                                                                                          ccGCGATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGacc                                                                                         <  2:1405349/101‑1 (MQ=255)  cgcgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCa                                                                                        >  1:103084/1‑101 (MQ=255)    cgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAgg                                                                                      <  1:196779/101‑1 (MQ=255)    cgATGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAgg                                                                                      <  2:891984/101‑1 (MQ=255)      aTGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGtt                                                                                    <  2:1057145/101‑1 (MQ=255)       tGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTa                                                                                   >  1:1046513/1‑101 (MQ=255)       tGGTTCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTa                                                                                   <  1:773091/101‑1 (MQ=255)        ggttCCGGTATCTGGACCATCTGTCGTGGTGCCACAATGGTGGATGGCAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa                                                                                  >  2:202164/4‑101 (MQ=255)        ggttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa                                                                                  <  1:863838/98‑1 (MQ=255)        ggttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTaa                                                                                  >  1:1079338/4‑101 (MQ=255)         gttCCGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAAc                                                                                 >  1:1525428/3‑101 (MQ=255)             cGGTATATGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGcta                                                                             <  1:1557336/101‑3 (MQ=255)              ggtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAt                                                                            <  2:1302635/98‑1 (MQ=255)               gtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAtt                                                                           >  1:830573/3‑101 (MQ=255)               gtatatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTAtt                                                                           >  2:1479118/3‑101 (MQ=255)                  tatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaa                                                                        <  2:754573/101‑2 (MQ=255)                  tatGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaa                                                                        <  2:630295/101‑2 (MQ=255)                   atGGACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGaac                                                                       <  2:1250661/101‑3 (MQ=255)                      gACCATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACgtg                                                                    >  2:678512/1‑99 (MQ=255)                         cATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATa                                                                 <  1:456782/101‑1 (MQ=255)                         cATCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATa                                                                 >  1:1343216/1‑101 (MQ=255)                          aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                <  2:1666489/101‑1 (MQ=255)                          aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                <  1:438007/101‑1 (MQ=255)                          aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                >  1:3315/1‑101 (MQ=255)                          aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                >  2:308636/1‑101 (MQ=255)                          aTCTGTCGTGGTGCCACAATGGTGGATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATaa                                                                >  2:1451688/1‑101 (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                                          >  2:1283315/1‑101 (MQ=255)                                                tggATGGTAAGCCCGTCATACCGGGAATGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAgcgc                                          >  1:939818/1‑101 (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                 <  1:896725/101‑3 (MQ=255)                                                                         aaTGAGGCTGTCGAAGGAAAAATGCGACCAGGTTAACGCTATTGAACGTGATAAGGCGCTGGCATGGGTGGAGCGCAATATTAAAGTACCACTGACCGaac                 <  1:202164/101‑3 (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)                                                                                                   |                                                                                          CCGCGATGGCTCCGGCATATGGACCATCTGTCGGGGAGCAACGATGGTGGACGGTAAACCTGTTATTCCGGGAATGAAACTGTCGAAGGAAAAATGCGCCCAGGTTAACGCCATTGAGCGGGATAAGGCGCTGGCATGGGTGGAGCGCAATATAAAAGTTCCACTGACCGAGCCACAGAAAGCCGGTA  >  178/1077‑1264

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: ‑