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%	63.1 / NA	22	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/8);  total (14/8)
*	NC_000913	480,296	0	G	A	95.5%	62.5 / NA	22	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (13/8);  minor base C (1/0);  total (14/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

ATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGT  >  NC_000913/480052‑480532                                                                                                                                                                                                                                                    ||                                                                                                                                                                                                                                             ataaACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTc                                                                                                                                                                                                                                        <  1:154397/251‑1 (MQ=255)         ccGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTAAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGGTAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATAc                                                                                                                                                                                                                                >  2:152390/1‑251 (MQ=255)                                                 aaTTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGGCGTAAACGCATTAAATAATCGGTTTTCGTTAAAACTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCg                                                                                                                                                                                        >  1:226403/1‑251 (MQ=255)                                                                                 aaGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGGAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGAGTCAATTGTCTGGCAACGGAGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATCCTTCAACCTATGGTTGTAATAATTCTAACAAGATAAACTAGCAGGATTCTCTTTCGTCGCATTGACAAcaca                                                                                                                                                         >  1:224253/2‑250 (MQ=255)                                                                                    tttATTCATGGTAAATTCGGCGAGACGGAGATATGCGGCTTAGTAAAATACCGCAACTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTCAATAATCGGTTTTCGTTAAAAATTTTTCGGACATCCTTCTACCTATGGTTGTAATAATTCTAACAAACTAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACgg                                                                                                                                                     >  2:348986/1‑251 (MQ=255)                                                                                                                             aGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTg                                                                                                            >  1:25459/1‑251 (MQ=255)                                                                                                                               tAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGc                                                                                                           >  1:361910/1‑250 (MQ=255)                                                                                                                                    tACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATAtt                                                                                                      >  1:318345/1‑250 (MQ=255)                                                                                                                                                      tGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGaac                                                                                   >  2:150912/1‑251 (MQ=255)                                                                                                                                                                   ttatttTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGgtgt                                                                      >  1:384088/1‑251 (MQ=255)                                                                                                                                                                         ttCTCGATAACCCGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATcc                                                                 <  2:318345/250‑1 (MQ=255)                                                                                                                                                                                 aaCACGCTCCAGAGAGTCAATTGTCTGGCAACGACGTAAACGCATCAAATCATAGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATCATTCTAACACGATAAACTAGCAGGATTCTCTTTCGTCGCATTGACAAAACTACGGAATAGTCGATTACCTGACTTCCGACATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATCAAGGTGTCATCCAGATATtcg                                                        >  2:380986/1‑251 (MQ=255)                                                                                                                                                                                         ccAGCGTCTCAATTGTCTGGCAACGATGTCAACTCATTAAATAATCGGTTTTCGGTAAAAATTTTTCGGACATTCTTTTCCCTATGGTTGTAATAACTCTAACAAGATCAACTCGCAGGATTCTCTTTCTTCGCATTGACAAAACAACGGAATAGTCTATTACCTGACTTCCGCCATTTCTGAAGATCCAGCATATTAATACCATAACTCCGCAACAACTTAAAGGTGTCATCCATATATTCGGCGATCTg                                                <  2:278765/251‑1 (MQ=255)                                                                                                                                                                                                            gCAACGAAGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCt                             >  2:26780/1‑251 (MQ=255)                                                                                                                                                                                                              aaCGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTc                           >  1:150494/1‑251 (MQ=255)                                                                                                                                                                                                                  acttAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATta                       <  1:331948/248‑1 (MQ=255)                                                                                                                                                                                                                       aaCGCATTAAATCATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGACGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATTCAGATATTCGTCGATCTGCTCACTGAGCTTATTGTCTTCATTATACtt                  >  2:335770/1‑251 (MQ=255)                                                                                                                                                                                                                         cGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGTATTCTCTTTCGTCGCATTGACAAAACAACGTAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAACTCCATAACTACTGAACAACATAAAGGTGTCTTTCAGATATTCGTCGATCTGCTCAATGATCTTATTTTCGGCATTATACTTaa                <  2:404074/251‑1 (MQ=255)                                                                                                                                                                                                                             ttAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAAtttt            >  2:152620/1‑251 (MQ=255)                                                                                                                                                                                                                                aataatCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTa         <  1:16939/251‑1 (MQ=255)                                                                                                                                                                                                                                       ggTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGt  <  2:87855/251‑1 (MQ=255)                                                                                                                                                                                                                                       ggTTTTCGATAAAAATTTTTCGGACATTCTTCAACCTATCGTTGTAATAATTAAAACAAGATAATCTCGCAGGATGCTCTTGCGTCGCATTGACAAAACAACGGATTAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCGGCATAGTAATACCATAACTTCTTAACAACAGAAATGTTTCATCCACTTATGCGTCGAACTGGTCAATGACCTTATGGTCGTTATTATACCTAATTTTGTTATTaatt  <  2:133875/251‑3 (MQ=255)                                                                                                                                                                                                                                                    ||                                                                                                                                                                                                                                             ATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGT  >  NC_000913/480052‑480532

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑