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	90.5%	55.4 / 0.0	21	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base A (10/9);  total (12/9)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.78e-01
*	NC_000913	480,296	0	G	A	90.5%	55.0 / ‑0.4	21	P5F (CCT→TTT)	hha	hemolysin expression‑modulating protein Hha
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base A (10/9);  total (12/9)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01

CGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGTGCGAAGGT  >  NC_000913/480079‑480540                                                                                                                                                                                                                         ||                                                                                                                                                                                                                                                     cGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGtaat                                                                                                                                                                                                                     >  1:274856/1‑251 (MQ=255)   aaTTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGtaataa                                                                                                                                                                                                                   <  1:146780/251‑1 (MQ=255)                  aaTAAATTTCTATACTGAGTAAGGGATCTTGTCGTACAGTTTTTTTATTGACAATTCGGCGTGTCGGGTATCTGCGGCTGAGTAAAATTCCGCCAGTTCATTATCTGATAATTCGTATTTATTTGTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAAAGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTTCCTATGGTTGTAATAATTCGAACAAGATaaa                                                                                                                                                                                                    <  2:187356/251‑1 (MQ=255)                      aaTTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGCGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATAATTATACCTATAGTTGTAATAATTCTAACAAGATAAACTCg                                                                                                                                                                                                >  1:86985/1‑251 (MQ=255)                         atcaatagtGAGGAATGGATATTGTCGTAAAGTTTAGTCATGGACAATTCGGCGAGGCGGTTATATGCGGCTGAGAAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGATGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTGTTCGGACATACTTCTACCTATGGTTGTAATAATTCTATCAAGATAAACTCGCa                                                                                                                                                                                              <  1:178721/242‑1 (MQ=255)                                                 tCGTACAGTTTATTCATGATCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACa                                                                                                                                                                      >  1:92329/1‑250 (MQ=255)                                                           tATTCATGGGCAATTCGGCGAGGCGGTGATCGGCGGCTGATTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTCAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGa                                                                                                                                                            <  1:80242/250‑1 (MQ=255)                                                               aagggtaaaTTCGGCGAGGCGGTGATCTGCGGCTGAGAAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGt                                                                                                                                                       <  2:130546/244‑1 (MQ=255)                                                                                                     aaaaTACCGTCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACTCATTAAATAATCGTTTTTCGTTAAAAATTTTTCGGACATTCTTCTTCCTATGGTTGTAATAATTCTAACAAGATAAACGCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCat                                                                                                                 <  2:338867/251‑1 (MQ=255)                                                                                                        aTACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATAtt                                                                                                              >  1:309808/1‑251 (MQ=255)                                                                                                         tACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGa                                                                                                                                                                                                                                             >  2:205497/1‑123 (MQ=255)                                                                                                                aGTTCATTATCGGATAATTCGTATTTATTTTTCTCGATAACACTCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTTCCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCAt                                                                                                      <  2:82081/251‑1 (MQ=255)                                                                                                                 gTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGCCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTGTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGAGCCTGCATATTAATACCATa                                                                                                     <  1:153146/251‑1 (MQ=255)                                                                                                                           tgatgaTTCGTATTTATTTTTCTCGATAACACGCTCCCGCGTGTCCATTGGCTGGCACCGACGTAAACGCATTAGATAATCGGTTTTCGTTAACAATTTTTCGGACCTACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCAATTTCTGAAGATCCTGCATATTATTACACTACCTACTGacc                                                                                           >  2:229968/1‑249 (MQ=255)                                                                                                                              tAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTAAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTAACTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTAGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACAATAACTACTGaacaac                                                                                        >  1:267511/1‑251 (MQ=255)                                                                                                                                 ttCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACAt                                                                                      >  2:165639/1‑250 (MQ=255)                                                                                                                                                              ccAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGTTTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTAATCCAGATATTCGTCGATCTg                                                        >  2:240607/1‑251 (MQ=255)                                                                                                                                                                atcGTGTCAATTGTCTTGCAACGACTTAATCGCATTAAATAATCGGGTTTCCTTCAAAATTTTTCGGACATTCTTCCACCTATGGTTGTAATAATTCTAACAATATAAACTCTCAGTCTCCTATTTCGTCGCATTTACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTAAAGATCCTGCATATTAATTCCATAACTACTGAACAACATAAAGGTGTTATCCAGATAGTCGTCTATCTgtt                                                      <  2:253126/249‑3 (MQ=255)                                                                                                                                                                          ttGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCtt                                            >  1:145973/1‑251 (MQ=255)                                                                                                                                                                                            aaCGCATTAAATAATCGGTTTTCGTTAAAAATTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACtt                          >  1:155904/1‑251 (MQ=255)                                                                                                                                                                                                                    ttAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAATGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGTGCGAAGGt  >  2:195370/1‑251 (MQ=255)                                                                                                                                                                                                                         ||                                                                                                                                                                                                                                                     CGAATTATTTATTAGCGAATAAATTTCCATACTGAGGAAGGGATCTTGTCGTACAGTTTATTCATGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAATTCGTATTTATTTTTCTCGATAACACGCTCCAGCGTGTCAATTGTCTGGCAACGACGTAAACGCATTAAATAATCGGTTTTCGTTAAAGGTTTTTCGGACATACTTCTACCTATGGTTGTAATAATTCTAACAAGATAAACTCGCAGGATTCTCTTTCGTCGCATTGACAAAACAACGGAATAGTCGATTACCTGACTTCCGCCATTTCTGAAGATCCTGCATATTAATACCATAACTACTGAACAACATAAAGGTGTCATCCAGATATTCGTCGATCTGCTCAATGAGCTTATTGTCTTCATTATACTTAATTTTGTAATTAAGTGCGAAGGT  >  NC_000913/480079‑480540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑