Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,644,142	G→A	Q55* (CAG→TAG)	ydfU ←	Qin prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,644,142	0	G	A	100.0%	65.6 / NA	20	Q55* (CAG→TAG)	ydfU	Qin prophage, uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/10);  total (10/10)

TCGCCATTAGGCCACTGGCAGGATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTGGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGCCCGGCTTAAGGACCACCAGCCCAAGC  >  NC_000913/1644009‑1644269                                                                                                                                      |                                                                                                                                tCGCCATTAGGCCACTGGCAGGATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAAACACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGaa                                                                                                                            <  1:399617/139‑1 (MQ=255)  cGCCATTAGGCCACTGGCAGGATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAAc                                                                                                                           >  1:99009/1‑139 (MQ=255)       ttAGGCCACTGGCAGGATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAg                                                                                                                      >  2:389862/1‑139 (MQ=255)                      gATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATg                                                                                                       <  1:209964/139‑1 (MQ=255)                           aaCATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGa                                                                                                  <  2:99009/139‑1 (MQ=255)                                 aCGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGc                                                                                            >  1:226979/1‑139 (MQ=255)                                  cGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCa                                                                                           >  2:238067/1‑139 (MQ=255)                                  cGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCa                                                                                           >  1:213746/1‑139 (MQ=255)                                           cAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTg                                                                                  >  1:157815/1‑139 (MQ=255)                                                         gcCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTccacc                                                                    <  2:120862/139‑1 (MQ=255)                                                           cAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAg                                                                  <  2:428803/139‑1 (MQ=255)                                                                 cgccAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCg                                                            <  1:411353/139‑1 (MQ=255)                                                                              aaTCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAat                                               <  2:90395/139‑1 (MQ=255)                                                                                tCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAatat                                             <  1:373141/139‑1 (MQ=255)                                                                                tCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAatat                                             <  2:140911/139‑1 (MQ=255)                                                                                                 aaaaaCGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGc                            >  2:495191/1‑139 (MQ=255)                                                                                                    aaCGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGcc                           <  1:441632/137‑1 (MQ=255)                                                                                                    aaCGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGcc                           >  2:441632/1‑137 (MQ=255)                                                                                                                      tCTTCCGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGCCCGGCTTAAGGACCACCAGcc       >  1:277908/1‑139 (MQ=255)                                                                                                                           cGCCAGCGGCTAGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGCCCGGCTTAAGGACCACCAGCCCAAGc  >  2:167255/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                TCGCCATTAGGCCACTGGCAGGATGTAACATGACGTAATAGCCAGTCGGACAATGCGCCAACGCCGCCAGCAGCACGAATCACCCGTTCGTTACTAAAAAACGGCAGCAATGTTTTGTCTTCCGCCAGCGGCTGGCGAACGGCAGGAACGACTCCGGATGGCAGATTACGCATGCTTTTTGGTTCCGGTTCCACCAGCACTCGAGGATTATGAAATATCTGTATGGATTCACGGCCCGGCTTAAGGACCACCAGCCCAAGC  >  NC_000913/1644009‑1644269

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑