Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	480,295	2 bp→AA	coding (13‑14/219 nt)	hha ←	hemolysin expression‑modulating protein Hha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	480,295	0	G	A	100.0%	54.9 / NA	18	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/7);  total (11/7)
*	NC_000913	480,296	0	G	A	100.0%	49.2 / NA	18	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/7);  total (11/7)

CGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTA  >  NC_000913/480073‑480529                                                                                                                                                                                                                               ||                                                                                                                                                                                                                                          cGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGt                                                                                                                                                                                                                >  2:17176/1‑251 (MQ=255)             atttattAGCGAATAAATTTACATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCGGATTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCt                                                                                                                                                                                                    <  2:69884/251‑1 (MQ=255)                     gCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGAt                                                                                                                                                                                            <  1:117669/251‑1 (MQ=255)                               ttCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGc                                                                                                                                                                                    >  2:17857/1‑249 (MQ=255)                                                               tttATTCATGGTCAATTCGGCGAGGCGGTGATTTGCGGCTGGGTAAAATACCGCCCGTTCATTATCTGTTAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTATAACAAGATAAACTAGCAGGATTCTCTTTCGTAGCATTGACAAAACAACgg                                                                                                                                                  >  2:142865/1‑251 (MQ=255)                                                                   ttCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTTAAATACCGCCAGTTCATTATCTGATAATTCGTATTTCTTTTTATCGATAACACGCTCCAGCGTGTCAATTGTGTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCCGGATTTTCTTTCGTCGCATTGACAAAACAACGGAAt                                                                                                                                               >  2:179831/1‑250 (MQ=255)                                                                                                                   gacAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACACTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTATAACAAGATAAACTCGCAGGATTCTCTTTCGTCTCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATAc                                                                                              >  1:142854/3‑251 (MQ=255)                                                                                                                                                atttTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATGAATACCATAACTACTGAACAACATAAAGGTGTCa                                                                 <  2:148868/251‑1 (MQ=255)                                                                                                                                                            aaCACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATtc                                                      <  1:173461/250‑1 (MQ=255)                                                                                                                                                              cacGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATAATTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATtcgtc                                                   >  1:30418/1‑251 (MQ=255)                                                                                                                                                                   tacagagagtccaTTGTCTGGCTACGGCGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTCTAATAATTCTAACAAGATAAACTCACAGGATTCTCTTTCGTCGCATTGACAAAACAACGGACTAGTCGATTCCCTGACTTACGCCCTATCTGCAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCAAGATATTCCTCGATCt                                              >  2:220531/13‑251 (MQ=255)                                                                                                                                                                       gCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGCTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGGGTCATCCAGATATTCGTCGATCTGCTc                                          >  2:50152/1‑251 (MQ=255)                                                                                                                                                                                      ggCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGCCATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGGCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTg                             <  2:142854/249‑1 (MQ=255)                                                                                                                                                                                      ggCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTAGGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCGGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACGACTGAACAACATAAAGGTGTCATCCAGATATGCGTCGATCTGCGCAATGAGCGTATTGTc                           <  2:139390/251‑1 (MQ=255)                                                                                                                                                                                                      cATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAAtt           >  1:1613/1‑251 (MQ=255)                                                                                                                                                                                                          aaaTAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCGTATTGTCTTCATTATACTTAATTTTGt       <  2:187458/251‑1 (MQ=255)                                                                                                                                                                                                              aatCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAAtt   >  2:180262/1‑251 (MQ=255)                                                                                                                                                                                                                 cGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTa  >  1:78449/1‑249 (MQ=255)                                                                                                                                                                                                                               ||                                                                                                                                                                                                                                          CGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTA  >  NC_000913/480073‑480529

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑