Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,643,727	(T)6→5	coding (578/1050 nt)	ydfU ←	Qin prophage; protein YdfU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,643,722	0	T	.	100.0%	82.5 / NA	20	coding (583/1050 nt)	ydfU	Qin prophage; protein YdfU
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (9/11);  total (9/11)

TGTTTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGC  >  NC_000913/1643655‑1643797                                                                    |                                                                            tgttTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGt                                                                >  1:299314/1‑80 (MQ=255)  gttTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTaa                                                              >  2:299306/1‑81 (MQ=255)   tttCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTaa                                                              <  2:299284/80‑1 (MQ=255)       aaTATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCa                                                         <  2:299285/81‑1 (MQ=255)        atatGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAg                                                        >  2:299312/1‑81 (MQ=255)           tGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCg                                                      <  1:299286/80‑1 (MQ=255)                gtggCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAacgac                                                <  1:299287/81‑1 (MQ=255)                gtggCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAacgac                                                <  2:299288/81‑1 (MQ=255)                gtggCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAacgac                                                >  1:299310/1‑81 (MQ=255)                     ggTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGAt                                           <  1:299289/81‑1 (MQ=255)                         aGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACa                                        <  1:299290/80‑1 (MQ=255)                           ctctCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGcc                                     >  1:299309/1‑81 (MQ=255)                            tctcCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCt                                    >  2:299327/1‑81 (MQ=255)                              tcCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCt                                    <  2:299291/79‑1 (MQ=255)                                 cGGTACGATGTCGCTTTCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGt                               <  1:299292/81‑1 (MQ=255)                                                 tCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCcaccac                 <  2:299293/79‑1 (MQ=255)                                                 tCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCt               >  1:299311/1‑81 (MQ=255)                                                 tCGCGGTACACCGAGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCt               >  2:299322/1‑81 (MQ=255)                                                     ggTACACCGAGCAGA‑TTTCTCCGCTGGTAATCCCAGCGAACGACGCGATATAGCCTCAGGTAGTGCATCCACCACCTGAtt           >  2:299315/1‑81 (MQ=255)                                                              aGCAGA‑TTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGc  <  1:299294/81‑1 (MQ=255)                                                                    |                                                                            TGTTTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGC  >  NC_000913/1643655‑1643797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑