Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,474	0	T	A	79.6%	88.0 / 19.4	50	intergenic (+478/‑105)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base T (9/1);  new base A (39/0);  total (49/1)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01

TTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTT  >  NC_007790/1378‑1556                                                                                                  |                                                                                     tttGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGA‑tt                                                                                 >  1:3360887/1‑99 (MQ=255) tttGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGA‑tt                                                                                 >  1:5932351/1‑99 (MQ=255)    gCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGA‑tttac                                                                              >  1:3012979/1‑96 (MQ=255)     cTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCCCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGA‑tttacc                                                                             >  1:4451113/1‑95 (MQ=255)                   tgtgAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAC‑ATGATTTA‑CCCCTAAACCTTTaaa                                                               >  1:4461602/1‑100 (MQ=255)                   tgtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTaaa                                                               >  1:3871354/1‑100 (MQ=255)                    gtgAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTaaaa                                                              >  1:3727713/1‑100 (MQ=255)                    gtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTaaaa                                                              >  1:3783862/1‑100 (MQ=255)                    gtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTaaaa                                                              >  1:1984657/1‑100 (MQ=255)                         aTTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAACCTAT‑AAGATTTA‑CCTCTAATTCTTTAAAATAccc                                                         >  1:890450/1‑100 (MQ=255)                         aTTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccc                                                         >  1:5853346/1‑100 (MQ=255)                         aTTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccc                                                         >  1:121581/1‑100 (MQ=255)                          acaCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑AAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccct                                                        >  1:5012557/3‑99 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATGGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:1217471/1‑98 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:2838827/1‑98 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:2496642/1‑98 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:2060975/1‑98 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:189483/1‑98 (MQ=255)                           tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                       >  1:121878/1‑98 (MQ=255)                            agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                                                      >  1:328609/3‑98 (MQ=255)                            agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                                                      >  1:3402249/3‑98 (MQ=255)                            aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                                                      >  1:5063431/1‑100 (MQ=255)                            aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                                                      >  1:3791734/1‑100 (MQ=255)                            aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                                                      >  1:3105097/1‑100 (MQ=255)                            aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                                                      >  1:2917194/1‑100 (MQ=255)                             ccATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCtt                                                     >  1:259409/1‑100 (MQ=255)                                       atttGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAAT‑GCCCCTTAAAATTCaaaa                                          >  1:3121297/1‑100 (MQ=255)                                       atttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGGTTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCaaa                                           >  1:28875/1‑100 (MQ=255)                                       atttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCaaa                                           >  1:4557846/1‑100 (MQ=255)                                        cttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCaaaa                                          >  1:919550/2‑100 (MQ=255)                                         ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                         >  1:424797/1‑100 (MQ=255)                                         ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                         >  1:1747726/1‑100 (MQ=255)                                         ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                         >  1:4967305/1‑100 (MQ=255)                                         ctGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                         >  1:3895711/2‑100 (MQ=255)                                          tagCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAAT‑GCCCCTTAAAATTCAAAATaa                                       >  1:2858025/3‑100 (MQ=255)                                          tGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAAT‑GCCCCTTAAAATTCAAAATaa                                       >  1:665836/1‑100 (MQ=255)                                          tGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAAT‑GCCCCTTAAAATTCAAAATaa                                       >  1:1992382/1‑100 (MQ=255)                                          tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa                                        >  1:4244771/1‑100 (MQ=255)                                          tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa                                        >  1:2783531/1‑100 (MQ=255)                                          tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa                                        >  1:1335662/1‑100 (MQ=255)                                          tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGA‑TTTACCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa                                        >  1:974312/1‑100 (MQ=255)                                           ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTATAAGGT‑TTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                       >  1:1240371/1‑100 (MQ=255)                                           ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                       >  1:4658108/1‑100 (MQ=255)                                           ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                       >  1:4299006/1‑100 (MQ=255)                                           ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                       >  1:4199925/1‑100 (MQ=255)                                           cccTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                       >  1:4976849/3‑100 (MQ=255)                                               cATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCACTTAAAATTCAAAATAACGGt                                   >  1:4301990/1‑100 (MQ=255)                                                gggggtGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATAAAGGtg                                  >  1:3925877/6‑99 (MQ=255)                                                 tatTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAAT‑GCCCCTTAAAATTCAAAATAAGGGCAtg                                <  1:5984109/100‑2 (MQ=255)                                                                                 atgtaggaaaaCTAT‑ATGATTTA‑CCCCTAAATCTTTAAAATACCCCCTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGtt  >  1:802396/8‑100 (MQ=255)                                                                                                  |                                                                                     TTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTT  >  NC_007790/1378‑1556

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: ‑