Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,476	1	.	T	79.0%	43.7 / 7.0	19	intergenic (+480/‑103)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base . (3/1);  new base T (15/0);  total (18/1)
Fisher's exact test for biased strand distribution p-value = 2.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01

TTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑C‑CCC‑CTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTAT  >  NC_007790/1377‑1525                                                                                                      |                                                     ccttGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑t                                                     >  1:3668955/3‑100 (MQ=255)   ttGCTGAAA‑TTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑ttta                                                  >  1:2203626/1‑97 (MQ=255)    tGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑ttta                                                  >  1:1809959/1‑97 (MQ=255)     gCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                                                 >  1:2000266/1‑96 (MQ=255)     gCTAAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                                                 >  1:1398334/1‑96 (MQ=255)     acggAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                                                 >  1:52174/4‑96 (MQ=255)                   ttgtGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTaa                                 >  1:4013432/1‑100 (MQ=255)                     gtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTaaaa                               >  1:4084218/1‑100 (MQ=255)                           ttAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTAAAATGcccc                         >  1:1853242/1‑100 (MQ=255)                            tagcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTAAAATGcccct                        >  1:3610816/4‑99 (MQ=255)                            tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TTTA‑CCT‑CTAAATCTTTAAAATAccctc                        >  1:3535992/1‑98 (MQ=255)                            gaCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGGTTTTTAAGTAG‑AAAA‑CTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATAccctc                        >  1:4359420/2‑98 (MQ=255)                             agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTAAAATGcccctt                       >  1:3315975/3‑98 (MQ=255)                             agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTAAAATGcccctt                       >  1:3831423/3‑98 (MQ=255)                             aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCctct                       >  1:1405439/1‑100 (MQ=255)                                    atttatttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTCTTaaaatt                >  1:4629165/1‑98 (MQ=255)                                      ttatttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TTTA‑CCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCa              >  1:203965/1‑100 (MQ=255)                                        ccttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCaaa            >  1:5032882/3‑100 (MQ=255)                                        atttGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATG‑GAAAAATATATGATTT‑A‑CCC‑CTAAACCTTTAAAAT‑GCCCCTTAAAATTCAAAAt          >  1:4067522/1‑100 (MQ=255)                                        atttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCaaa            >  1:4120700/1‑100 (MQ=255)                                         cttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCaaaa           >  1:2503208/2‑100 (MQ=255)                                           tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAA‑CTATAAGA‑TT‑TACCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa         >  1:1831520/1‑100 (MQ=255)                                           tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTGTTAAAATTCGAAATa         >  1:2193689/1‑100 (MQ=255)                                            ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGT‑‑‑AGAA‑CTATAAGATTT‑A‑CCT‑CTAAATCTTTAAAATACCCTCTTAAAATTCAAAATAAAg      >  1:3071619/1‑100 (MQ=255)                                                  tcttagCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TT‑T‑ACCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATAAAGGtgt  <  1:4539785/95‑3 (MQ=255)                                                                                                      |                                                     TTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑C‑CCC‑CTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTAT  >  NC_007790/1377‑1525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑