Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	503,675	0	A	T	66.7%	14.7 / 10.7	20	noncoding (25/93 nt)	SAUSA300_RS02390	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (5/1);  new base T (12/0);  total (19/1)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01

TGTGGTAATCATGTAATGCTTAAAAACAATATTGACTTTTACAGAACGTTCATATATGATAAATATTGTGTTTAGGAGGAATACCCAAGTCCGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCTATATA  >  NC_007793/503577‑503769                                                                                                   |                                                                                               tgtgGTAATCATGTCATGCTTAAAAACAATATTGACTTTTACAGAACGTTCATATATGATAAATATTGTGTTTAGGAGGAATACCCAAGTCCGGCTGAAg                                                                                               <  1:4653239/100‑1 (MQ=255)    ggTAATCATGTAATGCTTAAAAACAATATTGACTTTTACAGAACGTTCATATATGATAAATATTGTGTTTAGGAGGAATACCCAAGTCCGGCTGAAgaga                                                                                            >  1:349164/1‑100 (MQ=255)             gTAATGCTTAAAAACAATATTGACTTTTACAGAACGTTCATATATGATAAATATTGTGTTTAGGAGGAATACCCAAGTCCGGCT‑AAGAGATCggaagagc                                                                                  >  1:5423502/1‑94 (MQ=255)                                                                ccgtgtgTTTAGGAGGAATACCCAAGTCCGGCTGAGGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGGTCGAATCCCTCTtcctcc                                >  1:3280239/4‑100 (MQ=255)                                                                   agtgtTTAGGAGGAATACCCAAGTCCGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGcc                             >  1:1231084/2‑100 (MQ=255)                                                                    gtgtTTAGGAGGAATACCCAAGTCCGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGGTCGAATCCCTCTTCCTCCGCCa                            >  1:3112318/1‑100 (MQ=255)                                                                                 ctACCCAAGTCCGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTatat               >  1:5344163/2‑100 (MQ=255)                                                                                    cccAAGTCCGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTaa            >  1:1982909/1‑100 (MQ=255)                                                                                        aGTCCGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTtaaaaagaagat        >  1:3073981/1‑90 (MQ=14)                                                                                         gTCCGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCt       >  1:1432131/1‑100 (MQ=255)                                                                                           gcGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGGTCGAATCCCTCCTCCTCCGCCATCAATATTTATATTAAATTCtat     >  1:226700/2‑100 (MQ=255)                                                                                           ccGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCtat     >  1:3381013/1‑100 (MQ=255)                                                                                           ccGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAAACCCTCTTCCTCCGCCATCAATATTTATATTAAATTCtat     >  1:3077301/1‑100 (MQ=255)                                                                                           ccGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGATCTCATCCCTCTTCCTCCGCCAACAACATTTATATTAAATTCtat     >  1:4048337/1‑100 (MQ=17)                                                                                            cGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCtata    >  1:1721166/1‑100 (MQ=255)                                                                                            cGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCtaca    >  1:1048347/1‑98 (MQ=255)                                                                                            cGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCCCCATCAATATTTATATTAAATTCtata    >  1:1549020/1‑100 (MQ=255)                                                                                            cGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGGTCGAATCCCTCTTCCTCCGCCATCAATATTTTTATTAAATTCtata    >  1:5138313/1‑100 (MQ=255)                                                                                            cGGCTGATGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGAGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAAGTcaaag    >  1:4225509/1‑96 (MQ=17)                                                                                              gCTGAGGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGGTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCtatata  >  1:4214615/1‑100 (MQ=255)                                                                                                   |                                                                                               TGTGGTAATCATGTAATGCTTAAAAACAATATTGACTTTTACAGAACGTTCATATATGATAAATATTGTGTTTAGGAGGAATACCCAAGTCCGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGCTTAACGGCTCGCGGGGGTTCGAATCCCTCTTCCTCCGCCATCAATATTTATATTAAATTCTATATA  >  NC_007793/503577‑503769

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑