Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,485,638	T→A	L422* (TTA→TAA)	evgS →	sensor histidine kinase EvgS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,485,638	0	T	A	82.3%	27.2 / 3.5	17	L422* (TTA→TAA)	evgS	sensor histidine kinase EvgS
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base A (6/8);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 5.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.58e-01

GGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCGGA  >  NC_000913/2485391‑2485846                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                 ggTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGATTGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTaa                                                                                                                                                                                                                >  2:86184/1‑250 (MQ=255)           tttCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATc                                                                                                                                                                                                    >  1:94270/1‑251 (MQ=255)                   aTCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGtt                                                                                                                                                                                            >  1:165007/1‑251 (MQ=255)                                              ggAACACAGCTTAGCCCCGGAGGATTGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAgc                                                                                                                                                                 <  2:26329/251‑1 (MQ=255)                                                                  aggaTTGGATATAATACCTGGCGATATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGACGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCTCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTaa                                                                                                                                             <  1:89373/251‑1 (MQ=255)                                                                          atatAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTg                                                                                                                                     >  1:47340/1‑251 (MQ=255)                                                                                       cgcTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGctc                                                                                                                         <  1:86184/251‑1 (MQ=255)                                                                                                        aTCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTa                                                                                                        >  1:237112/1‑250 (MQ=255)                                                                                                          cGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAAt                                                                                                     <  2:47340/251‑1 (MQ=255)                                                                                                                                                               tgttaTGCAAAAAGTGCCTTACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATGCCATATTATTATGAGCTGCATGCTCA‑TAAAAAGAGATGTATCCGGAGATTGAATGGATACAGGTCGATAATGCCAGCGCTGCGTTTCACAAGGTGAAGGAAGTTGAACTTGATGCCCTGGTCGCGACACATGTAAATTCGCGTTACATGAGCGATCATTACTATCCTAATGAACTTTATCATTTTCTTa                                                 <  1:128452/246‑1 (MQ=255)                                                                                                                                                                                    cAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATc                           >  1:106839/1‑251 (MQ=255)                                                                                                                                                                                        gAACAAACATTAAAAAAAGGAATGAAAGATGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTCTCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCCTTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCtt                       >  1:168772/1‑251 (MQ=255)                                                                                                                                                                                                      aaaaGGAATGAAAGTTGCCATTCCATATTATTATTGGCCGCAATCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCTACACAGCTAAATTCGCGTTACATGATCGATCAGTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTGCCGAATGCATCGCTTTCGTGCGCTTTTcc         <  2:235341/251‑1 (MQ=255)                                                                                                                                                                                                       aaaGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCAATCGCA‑GAAAAAGAGATGTATCCGGAGGGTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCt        <  2:102893/251‑1 (MQ=255)                                                                                                                                                                                                        aaGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTc       <  2:94270/251‑1 (MQ=255)                                                                                                                                                                                                             aTGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCA‑TAAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCGga  <  2:176433/251‑1 (MQ=255)                                                                                                                                                                                                              tGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCggg  >  1:58316/1‑250 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                 GGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCGGA  >  NC_000913/2485391‑2485846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑