Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	779,100	0	C	A	61.1%	4.7 / 14.7	19	intergenic (+15/+127)	SAUSA300_RS03775/SAUSA300_RS03780	lipoteichoic acid synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (7/0);  new base A (11/0);  total (19/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.29e-01

CTACAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATA  >  NC_007793/779004‑779164                                                                                                 |                                                                 cTACAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAAcaga                                                               >  1:2058706/1‑97 (MQ=255)   tcAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:5779623/2‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAGAGGTAACTCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:2136739/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTATACACGAGATCGGa                                                             >  1:2699166/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAGACACGAGATCGGa                                                             >  1:4825687/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAGACACGAGATCGGa                                                             >  1:380488/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAATCACGAGATCGGa                                                             >  1:55025/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAATCACGAGATCGGa                                                             >  1:4096869/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAGCACGAGATCGGa                                                             >  1:1019132/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:5968637/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:4956370/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:3405044/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:3201048/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAAcagatc                                                             >  1:3875176/1‑95 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:3398845/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:2924092/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:547276/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:5531511/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCAGa                                                             >  1:1289482/1‑100 (MQ=255)   aCAAAAATCCAGACTTCAAAAAGGGAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAGATCGGa                                                             >  1:2734964/1‑100 (MQ=255)           ccAGACTTCAAAAGGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAACCACGAGTTCGGaagagcaca                                                     >  1:5853949/1‑92 (MQ=255)                                                              aaaGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATtata  >  1:2413537/1‑100 (MQ=255)                                                                                                 |                                                                 CTACAAAAATCCAGACTTCAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATA  >  NC_007793/779004‑779164

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑