Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,918,625	G→A	S411S (TCC→TCT)	atpA ←	ATP synthase F1 complex subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,918,625	0	G	A	100.0%	159.8 / NA	44	S411S (TCC→TCT)	atpA	ATP synthase F1 complex subunit alpha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/18);  total (26/18)

GCATACTGTTTCTGTTTCAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCGGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGTTTTTTCA  >  NC_000913/3918548‑3918701                                                                              |                                                                             gcATACTGTTTCTGTTTCAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGAt                                                                           >  2:711990/1‑81 (MQ=255)   aTACTGTTTCTGTTTCAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATg                                                                          >  2:711992/1‑80 (MQ=255)      ctgtttctgtttCAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCaaa                                                                      >  2:711978/1‑81 (MQ=255)         tttctgtttcAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACt                                                                    <  2:711933/80‑1 (MQ=255)           tctgtttcAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACt                                                                    >  1:711997/1‑78 (MQ=255)              gtttcAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTgagag                                                               >  1:711995/1‑80 (MQ=255)               tttcAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGaa                                                             >  2:712005/1‑81 (MQ=255)                 tcAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACg                                                           >  2:712000/1‑81 (MQ=255)                   agcagTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCt                                                         <  1:711935/81‑1 (MQ=255)                   agcagTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCt                                                         >  1:712017/1‑81 (MQ=255)                     cagTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGc                                                       >  1:712003/1‑81 (MQ=255)                      agTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGc                                                       >  1:712000/1‑80 (MQ=255)                          cGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGt                                                   <  1:711936/80‑1 (MQ=255)                           ggTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTc                                                 <  2:711936/81‑1 (MQ=255)                               aCTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACg                                              <  2:711938/80‑1 (MQ=255)                                   tCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACt                                         >  1:712021/1‑81 (MQ=255)                                        ccGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGcc                                    <  2:711939/81‑1 (MQ=255)                                          gTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGc                                     >  1:712013/1‑78 (MQ=255)                                              tCAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCg                              <  1:711941/81‑1 (MQ=255)                                               cAAGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCgg                             >  1:712004/1‑81 (MQ=255)                                                aaGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCgg                             <  1:711943/80‑1 (MQ=255)                                                aaGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCgg                             <  2:711941/80‑1 (MQ=255)                                                 aGCTGCTTACGTGTTGCGTCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTa                           <  2:711943/81‑1 (MQ=255)                                                 aGCTGCTTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTa                           >  2:712006/1‑81 (MQ=255)                                                  gctgctTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTAc                          <  1:711945/81‑1 (MQ=255)                                                      ctTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGa                       <  1:711947/80‑1 (MQ=255)                                                      ctTACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGAt                      <  2:711945/81‑1 (MQ=255)                                                      ctTACGTGTTGCATCGTCAAGGTCAGATGCAAAATGAGAGAACGCTGCAAGTTCACGATACTGTGCCAGAGCGGTACGGAt                      <  1:711948/81‑1 (MQ=255)                                                       ttACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATa                     >  2:712017/1‑81 (MQ=255)                                                        tACGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATac                    >  2:712026/1‑81 (MQ=255)                                                         aCGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATac                    >  2:711998/1‑80 (MQ=255)                                                         aCGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATac                    >  1:712009/1‑80 (MQ=255)                                                         aCGTGTTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATa                     <  2:711948/79‑1 (MQ=255)                                                           gtgtTGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATaccac                 >  2:712023/1‑81 (MQ=255)                                                              ttGCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCg               >  1:712002/1‑80 (MQ=255)                                                                gCATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCTCTATACTGTGCCAGATCGGTACTTATACCACCGTAc            >  1:893667/1‑81 (MQ=255)                                                                 cATCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGa             >  1:711996/1‑79 (MQ=255)                                                                   tCGTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGt         <  2:711949/81‑1 (MQ=255)                                                                     gTCAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGttt       >  1:712010/1‑81 (MQ=255)                                                                       cAAGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGttttt     >  2:712010/1‑81 (MQ=255)                                                                        aaGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCTAGAGCGGTACGGATACCACCGGACAGtttttt    <  2:711950/81‑1 (MQ=255)                                                                        aaGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGtttttt    >  2:712018/1‑81 (MQ=255)                                                                        aaGGTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGttttt     <  1:711952/80‑1 (MQ=255)                                                                          ggTCAGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGTTTTTTCa  >  1:712008/1‑81 (MQ=255)                                                                              |                                                                             GCATACTGTTTCTGTTTCAGCAGTTCGGTCACTTTCTGACCGTGGTCAAGCTGCTTACGTGTTGCATCGTCAAGGTCGGATGCAAACTGAGAGAACGCTGCCAGTTCACGATACTGTGCCAGAGCGGTACGGATACCACCGGACAGTTTTTTCA  >  NC_000913/3918548‑3918701

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑