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%	38.8 / NA	15	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/6);  total (9/6)
*	NC_000913	480,296	0	G	A	100.0%	41.0 / NA	15	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/6);  total (9/6)

GCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGT  >  NC_000913/480069‑480532                                                                                                                                                                                                                                   ||                                                                                                                                                                                                                                              gCTCCGCAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCTGCCGGGTAAAATACCGCCAGTTCATTATCTGATCATTCGTTTTTATTTTTGTCGATAACACGCTCCAACGGTTTGATTTTCTGGCAACGACGTAAAAACATTAAATAATCGGATTTCGTTAAAAATTTTTCG‑ACAATACTTCTAcat                                                                                                                                                                                                                        >  2:166144/1‑248 (MQ=255)                                                     aTCTTGTCGTACGGTTTATTCATGGTAAATTCGGCGGGGCGGTGATTGGCGGCTGAGAAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTAc                                                                                                                                                                                                                          <  2:324287/196‑1 (MQ=255)                                                     aTCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTAc                                                                                                                                                                                                                          >  1:324287/1‑196 (MQ=255)                                                      tCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAAAACCGCCCGTTCATTATCTGAAAATTCGTATTTATTTTTCTCGCTAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTAGTTAAAAATTTTTCGGACA‑TAATTCTACCTATGGTTGCAATAATTCTAACAAGATAAACTCGCAGGATTTTCTTTCGTCGCAtt                                                                                                                                                                  >  1:184307/1‑251 (MQ=255)                                                                                              gTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGATGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCAt                                                                                                                          >  1:300209/1‑251 (MQ=255)                                                                                                          tataaaaaaTCCCGCCTGTGCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCGCCCGCGTGTCAATTGTCTGGCATCGACGTAACCGCATTAAATAATCGGTTTTCGTTAAAAATTTTGCTGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGTTGCTCTTTCGTCGCATTGAAAAAACAACGTAAAAGTCGATTACCTTACTTCCGCTATCTCTGAAGATc                                                                                                               <  2:208185/245‑1 (MQ=255)                                                                                                               aaaaTACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCat                                                                                                         >  1:187041/1‑251 (MQ=255)                                                                                                                             tCATTATCTGATAATTCGTATTTATTTTTCTCGATAACCCGCTCCAGCGTGTCAATTGTCTGGCAAAGACGTAAACGAATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGATGTAATAATTCTAACAAGATAAAATCGCAGGATTATCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACATAACTTCCGCAATTTCTAAAGATCCTGCA‑ATTaaatacattaac                                                                                          >  1:361457/1‑241 (MQ=255)                                                                                                                                            tCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAACCGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCatat                                                                                                       >  2:205122/1‑224 (MQ=255)                                                                                                                                            tCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCatat                                                                                                       <  1:205122/224‑1 (MQ=255)                                                                                                                                                            cGATAACACGCTCCAGCGTGTCAATTGACTGGCAACGACGTACACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCCTTGACAAAACAAAGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCATGCATATTACTACCATAATTACTGAACAACATAAAGGTGTCATCCAGat                                                             >  1:140409/1‑250 (MQ=255)                                                                                                                                                                  cacGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATtcgtc                                                      >  1:175383/1‑251 (MQ=255)                                                                                                                                                                              ggtCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAAt                                          <  1:209526/250‑1 (MQ=255)                                                                                                                                                                                           gCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCt                             <  1:234451/251‑1 (MQ=255)                                                                                                                                                                                                                      ggTTTTCGTTAAAAATTTTGCGGACA‑TACTTCTACCGATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGt  <  1:353747/251‑1 (MQ=255)                                                                                                                                                                                                                                   ||                                                                                                                                                                                                                                              GCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACA‑TACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGT  >  NC_000913/480069‑480532

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑