Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,301	1	.	G	76.7%	52.7 / 21.2	30	intergenic (+305/‑278)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base . (5/2);  new base G (7/16);  total (12/18)
Fisher's exact test for biased strand distribution p-value = 8.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.16e-01

ATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTG  >  NC_007790/1220‑1393                                                                                    |                                                                                               acgtagttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGAt                                                                             >  1:4691524/7‑100 (MQ=255)   gtagttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGCAGTTTTACAGGAttt                                                                           >  1:647344/5‑100 (MQ=255)     agttACGGAGTTCTTAGAGAAAAAATAAAACTTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTa                                                                         >  1:5871432/3‑100 (MQ=255)      gttgcGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTAt                                                                        >  1:1958292/5‑100 (MQ=255)        tACAGAGTTCTTAGAGATAAATTAAAAATTCTCGATTTTTGATAAAAACCGCTCTGCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGc                                                                      >  1:4018663/1‑100 (MQ=255)        caCGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGc                                                                      >  1:4617800/2‑100 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                           <  1:5422463/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                           <  1:5725020/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                           <  1:4980665/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                                           <  1:3865303/100‑1 (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                                          <  1:2036675/100‑1 (MQ=255)                                    ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa                                          <  1:1630375/100‑1 (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)                                                                                    |                                                                                               ATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTG  >  NC_007790/1220‑1393

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: ‑