Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,373	0	C	T	43.5%	9.2 / 58.1	62	intergenic (+377/‑206)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (25/10);  new base T (18/9);  total (43/19)
Fisher's exact test for biased strand distribution p-value = 7.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.17e-01

CCCTGCAGGAATTTAGAAAAACAT‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT  >  NC_007790/1278‑1472                                                                                                     |                                                                                                    tcttGCAGGAATTTAGAAAAACATGGG‑GGCAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTg                                                                                                   <  1:4595035/97‑1 (MQ=255)    tGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTgggt                                                                                                <  1:3712836/100‑3 (MQ=255)     gCAGGAATTTAGAAAAACAC‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                                            >  1:2361151/1‑100 (MQ=255)     gCAGGAATTTAGAAAAACAC‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                                            >  1:70742/1‑100 (MQ=255)      cAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                                                              <  1:112024/100‑1 (MQ=255)      cAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTAAGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                                                              <  1:5889750/100‑1 (MQ=255)       aGGAATTTAGAAAAACAC‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTg                                                                                          <  1:1402395/100‑1 (MQ=255)          gtgttAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TG‑TAAATGGGCAGTGTTTAAAAAAATAGTCATTGGttttattt                                                                                          >  1:5273308/4‑96 (MQ=255)                   aaaCAT‑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                              <  1:5835355/100‑1 (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                         <  1:1481097/100‑1 (MQ=255)                                                                             gggCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtat                         >  1:4994953/1‑100 (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)                                                                                         acaaaaTAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATAAGttttggat              <  1:2729505/98‑5 (MQ=255)                                                                                          aaaaTTAGTCACTGTTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGt             <  1:3054418/100‑1 (MQ=255)                                                                                          aaaaTTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGt             <  1:2777634/100‑1 (MQ=255)                                                                                              ctAGTCACTGGTTTTGCTGAAATTTTTGATTGTGAAATTACCATTTATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAgcagaa         >  1:5080547/2‑95 (MQ=255)                                                                                               tAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGtagaaa        >  1:1076036/1‑95 (MQ=255)                                                                                                  tgaCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAAct     >  1:3922156/3‑99 (MQ=255)                                                                                                   gaCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:5584677/2‑98 (MQ=255)                                                                                                   cccTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:5962046/3‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1728540/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1214567/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:4023402/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1532213/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1580960/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1714849/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:369687/1‑98 (MQ=255)                                                                                                   cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTCTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:1223666/1‑98 (MQ=255)                                                                                                   accTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:4316587/3‑98 (MQ=255)                                                                                                    aCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActat   >  1:3123018/1‑97 (MQ=255)                                                                                                     cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata  >  1:5031868/1‑96 (MQ=255)                                                                                                     cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata  >  1:2038748/1‑96 (MQ=255)                                                                                                     cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata  <  1:3299540/100‑5 (MQ=255)                                                                                                     cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata  >  1:2792540/1‑96 (MQ=255)                                                                                                     |                                                                                                    CCCTGCAGGAATTTAGAAAAACAT‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TG‑TAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT  >  NC_007790/1278‑1472

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: ‑