Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,361	0	A	C	30.4%	54.0 / 35.1	47	intergenic (+365/‑218)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (20/12);  new base C (10/4);  total (31/16)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.75e-01

AAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATA  >  NC_007790/1270‑1452                                                                                                  |                                                                                            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                    <  1:1916742/100‑1 (MQ=255)                                                                      aTTTGCATTT‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGt                    >  1:234257/1‑100 (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          <  1:5835355/100‑1 (MQ=255)                                                                                 tAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCt          >  1:4724165/1‑100 (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)                                                                                      accctgtg‑tTAAAAAATTAGTCACTGGATTTGCTGAAATTATTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGATTGtat     >  1:2951936/6‑100 (MQ=255)                                                                                       atcAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATCTGTATTTGGCTCATATTTTCGTTTTAAAAGCGtatataa   >  1:3463792/3‑99 (MQ=255)                                                                                         ttgtg‑tTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtataga  >  1:5431635/3‑98 (MQ=255)                                                                                                  |                                                                                            AAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATA  >  NC_007790/1270‑1452

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: ‑