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	95.5%	63.8 / NA	22	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (12/9);  minor base C (1/0);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	480,296	0	G	A	95.5%	62.0 / NA	22	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (12/9);  minor base C (1/0);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

AACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTA  >  NC_000913/480055‑480525                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                      aaCAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCCGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTTGTTAAAAATTTTTCgg                                                                                                                                                                                                                               >  2:416516/1‑250 (MQ=255)    aGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACAt                                                                                                                                                                                                                           <  1:416516/251‑1 (MQ=255)       cGGTTATAGCTCCGCAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACt                                                                                                                                                                                                                        >  1:381047/1‑251 (MQ=255)                     aaaGAGAATTATTTATTAGCGAATAAAGTTCCATTCTGAGGAAGGGATTTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTg                                                                                                                                                                                                          <  2:375262/251‑1 (MQ=255)                                tttattAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCCGTTCAATATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTTAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAACATTTTTCGGACTTACTTCTCCCTATGGTTTTAATAATTCt                                                                                                                                                                                                >  2:201287/1‑250 (MQ=255)                                 ttattaGCGAATAAATTTCCATACTGAGGCAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGGTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTATCGCTAACACGCTCCAGCGGGTCAATTGTCTGGCAACGACGTAAACGCATTACATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGATGTAATAATTCTa                                                                                                                                                                                               >  1:347016/1‑250 (MQ=255)                                             aaaTTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTc                                                                                                                                                                                  >  1:139968/1‑251 (MQ=255)                                              aaTTTCTATACTGAAAAAGGGATCTTGTCGAACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGCGTAAAATACCGCCAGTTTATTATCTGATAATTCGTATTTATTTTTCTCGATAAAACGCCCCCACGTGTCAATTGTCTGGCAACGACGTAAACGCATTTAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTAACTATGGTTGTAATAATTCTAACAAGATAAAATCg                                                                                                                                                                                 >  2:312095/1‑251 (MQ=255)                                                                                  taaTTCAGGGTCAATTCGGCGAGGCGGTGATCTGGGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAAGTGTCTGGCAACGACGTAAACGCATTAAATAAGCGGTTTTCGTTAAAAATTTTTCGGACATTCTTCTTCCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACgg                                                                                                                                              <  2:57346/248‑1 (MQ=255)                                                                                                               aTCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTAGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGCCGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAACACAACGGAATAGTCGATTACCTGACTTCCGCCATTTc                                                                                                                >  1:235461/1‑251 (MQ=255)                                                                                                                             aaaaTACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCat                                                                                                  >  2:4948/1‑251 (MQ=255)                                                                                                                                    cGCCAGATCATTATCTGTGAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAAt                                                                                            >  2:96130/1‑250 (MQ=255)                                                                                                                                                            gTATTTATTTTTCTCGATAACACGCTCCTCCGTGTCAATTGGCTGGCAAAGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATCCTTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTCACAAAACAACGGACTAGTCGATTAACTGACTTCCGCCATTTCTGCAGATCCTGCATATTAATACAATAACTAATGAAAAACATaa                                                                     >  2:25930/1‑249 (MQ=255)                                                                                                                                                            gTATTTATTTTTCTCGATAACACGATCCAGCGTGTCAATTGTCTGGCACCGTCGTAAACGCATTAAATAATCGGTTTTCGTTAAAACTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATaa                                                                     >  2:60133/1‑249 (MQ=255)                                                                                                                                                                          cGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAACTAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGat                                                      >  2:185948/1‑250 (MQ=255)                                                                                                                                                                          cGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAg                                                        <  2:278014/248‑1 (MQ=255)                                                                                                                                                                           gATAACACGCGCCAGCGTTTCAATTTTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTGCCTATGTTTGTAATAATTCTAATAAGAGAAACTCGCAGGAGCCTCTTTCGTCGCAGGGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTGCTGAAGATCCTGTATATGAGTACCATAGCTATTGAAGTACATAAAGGGGCCATCCAGatat                                                    <  2:28988/251‑1 (MQ=255)                                                                                                                                                                            aTAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATAtt                                                   <  1:120359/251‑1 (MQ=255)                                                                                                                                                                                  cGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGa                                             <  1:356351/251‑1 (MQ=255)                                                                                                                                                                                                        ggCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTAtt                          <  2:3977/248‑1 (MQ=255)                                                                                                                                                                                                        ggCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTAtt                          <  1:396673/248‑1 (MQ=255)                                                                                                                                                                                                                              ataatCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTa  >  1:210929/1‑250 (MQ=255)                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                      AACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTA  >  NC_000913/480055‑480525

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: ‑