Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,352	0	G	A	23.6%	68.8 / 20.0	55	intergenic (+356/‑227)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base G (18/24);  new base A (9/4);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.02e-02

ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTAT  >  NC_007790/1254‑1449                                                                                                        |                                                                                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGc                                                                                                   <  1:5422463/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGc                                                                                                   <  1:4980665/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGc                                                                                                   <  1:5725020/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGc                                                                                                   <  1:3226450/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGc                                                                                                   <  1:3865303/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAACGGGc                                                                                                   <  1:2249750/100‑1 (MQ=255) attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑GG‑GAAATGGGc                                                                                                   <  1:1760247/100‑1 (MQ=255)  ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCa                                                                                                  <  1:2036675/100‑1 (MQ=255)  ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCa                                                                                                  <  1:1630375/100‑1 (MQ=255)      tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAgtg                                                                                               <  1:3352581/96‑1 (MQ=255)      tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAAGGGGCAgat                                                                                               <  1:3152989/96‑3 (MQ=255)       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAATGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAgtgg                                                                                              <  1:4507874/97‑2 (MQ=255)       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAgcag                                                                                              >  1:3220985/4‑97 (MQ=255)                 aaaaaaTGTCTTGCAGGAATTTAGAAAAACAGG‑GG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTtaaaaaaat                                                                                   <  1:5734429/100‑4 (MQ=255)                    aaaCGCTCTGCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCat                                                                              >  1:2282828/1‑99 (MQ=255)                         tcttGCAGGAATTTAGAAAAACA‑TGGG‑GGCAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTg                                                                            <  1:4595035/97‑1 (MQ=255)                            tGCAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTgggt                                                                         <  1:3712836/100‑3 (MQ=255)                             gCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                     >  1:70742/1‑100 (MQ=255)                             gCAGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                     >  1:2361151/1‑100 (MQ=255)                              cAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                                       <  1:112024/100‑1 (MQ=255)                              cAGGAATTTAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTAAGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                                       <  1:5889750/100‑1 (MQ=255)                               aGGAATTTAGAAAAACA‑C‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTg                                                                   <  1:1402395/100‑1 (MQ=255)                                  gtgttAGAAAAACA‑TGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGttttattt                                                                   >  1:5273308/4‑96 (MQ=255)                                           aaaCA‑T‑GGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATtttg                                                          >  1:1910627/1‑100 (MQ=255)                                               aacacgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATTGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTtttgtttg                                                      >  1:3904576/10‑100 (MQ=255)                                                ccacgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTttgtttgt                                                     >  1:1200553/9‑100 (MQ=255)                                                acccgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTttgtttgt                                                     >  1:5161703/9‑100 (MQ=255)                                                   cgggaaaGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTtgtggg                                                  <  1:4447524/95‑3 (MQ=255)                                                                      tttATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATatgtatttt                               <  1:3138321/100‑2 (MQ=255)                                                                            cTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCat                         <  1:1320434/100‑1 (MQ=255)                                                                              aacttttAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGATTTATTTAAAATTTTGTTTTTGCAAATAGCATATATGTATTTGGCTCat                         >  1:5299883/4‑100 (MQ=255)                                                                                      aTTTGCATTT‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGt                 >  1:234257/1‑100 (MQ=255)                                                                                      aTTTGCATTT‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGt                 <  1:1916742/100‑1 (MQ=255)                                                                                       tttGCA‑TTTTAAATAGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTGCCATATATTTATTTGGCTCATATTTGCGtt                <  1:4403878/100‑1 (MQ=255)                                                                                        ttGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGttt               >  1:2790242/1‑100 (MQ=255)                                                                                        ttGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTa             >  1:1089256/1‑100 (MQ=255)                                                                                        gttgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGtt                >  1:2555550/10‑100 (MQ=255)                                                                                         ttgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAA‑TTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGtttg              <  1:569313/92‑2 (MQ=255)                                                                                         ttgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGttt               >  1:6071017/9‑100 (MQ=255)                                                                                         tGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGtttt              >  1:5506777/1‑100 (MQ=255)                                                                                         tGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTaa            >  1:4598084/1‑100 (MQ=255)                                                                                          tgcattttAAATGGGCAGTG‑TTAGAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGtttt              >  1:5363952/8‑100 (MQ=255)                                                                                          gCA‑TG‑TAAATGGGCAGTGTTTAAAAAGATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTa             >  1:4644893/1‑100 (MQ=255)                                                                                           gtgttttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTa             <  1:3475517/94‑1 (MQ=255)                                                                                           gcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTa             >  1:6050060/7‑100 (MQ=255)                                                                                           gcattttAAATGGGCAGTG‑TTAAAAAATTAGCCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTa             >  1:3277223/7‑100 (MQ=255)                                                                                             gtgtgaaaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAag           >  1:2430268/6‑100 (MQ=255)                                                                                               g‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAagag         >  1:3561516/1‑100 (MQ=255)                                                                                                 tAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCt       >  1:4724165/1‑100 (MQ=255)                                                                                                 tAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCt       <  1:5835355/100‑1 (MQ=255)                                                                                                  atctGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTTATATTTGCGTTTTAAGAGCta      <  1:1543543/97‑2 (MQ=255)                                                                                                   tctGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTg     >  1:884219/3‑100 (MQ=255)                                                                                                    ctGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAAGAGAtta     >  1:1910248/2‑99 (MQ=255)                                                                                                     tGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAA‑TTTTGTTTGTGAAATTACCATATATTTATTCGGCTCATATTTGCGTTTTAAGAGCTTGtat  <  1:1798132/100‑1 (MQ=255)                                                                                                     tGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTCGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGcgtaaga  >  1:997240/1‑94 (MQ=255)                                                                                                      gggCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAAGAGAttatg   >  1:2267324/1‑97 (MQ=255)                                                                                                      gggCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtat  >  1:4994953/1‑100 (MQ=255)                                                                                                      gggCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtat  <  1:1481097/100‑1 (MQ=255)                                                                                                        |                                                                                                   ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTAT  >  NC_007790/1254‑1449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑