Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,330	0	T	C	66.7%	24.2 / 15.9	30	intergenic (+334/‑249)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base T (6/4);  new base C (3/17);  total (9/21)
Fisher's exact test for biased strand distribution p-value = 3.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.01e-01

ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCAT  >  NC_007790/1254‑1426                                                                                |                                                                                                  attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                                                            <  1:3865303/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                                                            <  1:5725020/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                                                            <  1:5422463/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                                                            <  1:4980665/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                                                            <  1:3226450/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAACGGGc                                                                            <  1:2249750/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCAGGGAAATGGGc                                                                            <  1:1760247/100‑1 (MQ=255)  ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa                                                                           <  1:1630375/100‑1 (MQ=255)  ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa                                                                           <  1:2036675/100‑1 (MQ=255)      tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtg                                                                        <  1:3352581/96‑1 (MQ=255)      tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAAGGGGCAgat                                                                        <  1:3152989/96‑3 (MQ=255)       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAATGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtgg                                                                       <  1:4507874/97‑2 (MQ=255)       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgcag                                                                       >  1:3220985/4‑97 (MQ=255)                 aaaaaaTGTCTTGCAGGAATTTAGAAAAACAGG‑GG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTG‑TTtaaaaaaat                                                            <  1:5734429/100‑4 (MQ=255)                    aaaCGCTCTGCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCat                                                       >  1:2282828/1‑99 (MQ=255)                         tcttGCAGGAATTTAGAAAAACA‑TGGG‑GGCAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTg                                                     <  1:4595035/97‑1 (MQ=255)                            tGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTgggt                                                  <  1:3712836/100‑3 (MQ=255)                             gCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                              >  1:70742/1‑100 (MQ=255)                             gCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                              >  1:2361151/1‑100 (MQ=255)                              cAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                <  1:112024/100‑1 (MQ=255)                              cAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTAAGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                <  1:5889750/100‑1 (MQ=255)                               aGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTg                                            <  1:1402395/100‑1 (MQ=255)                                  gtgttAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGttttattt                                            >  1:5273308/4‑96 (MQ=255)                                           aaaCA‑T‑GGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATtttg                                   >  1:1910627/1‑100 (MQ=255)                                               aacacgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATTGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTtttgtttg                               >  1:3904576/10‑100 (MQ=255)                                                ccacgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTttgtttgt                              >  1:1200553/9‑100 (MQ=255)                                                acccgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTttgtttgt                              >  1:5161703/9‑100 (MQ=255)                                                   cgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTtgtggg                           <  1:4447524/95‑3 (MQ=255)                                                                      tttATGCTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATatgtatttt        <  1:3138321/100‑2 (MQ=255)                                                                            cTAATTTTTAATTTGCATGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCat  <  1:1320434/100‑1 (MQ=255)                                                                                |                                                                                                  ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCAT  >  NC_007790/1254‑1426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑