Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,463	0	A	G	46.7%	3.4 / 76.4	75	intergenic (+467/‑116)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (40/0);  new base G (32/3);  total (72/3)
Fisher's exact test for biased strand distribution p-value = 9.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

TCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATT  >  NC_007790/1370‑1526                                                                                              |                                                                   tgaCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAAct                                                              >  1:3922156/3‑99 (MQ=255)  gaCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:5584677/2‑98 (MQ=255)  cccTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:5962046/3‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:1214567/1‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:4023402/1‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:1728540/1‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:1714849/1‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:1580960/1‑98 (MQ=255)  cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa                                                             >  1:1532213/1‑98 (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)    cgatctttGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata                                                           <  1:3332494/95‑5 (MQ=255)    cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata                                                           <  1:3299540/100‑5 (MQ=255)    cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata                                                           >  1:2038748/1‑96 (MQ=255)    cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata                                                           >  1:2792540/1‑96 (MQ=255)    cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata                                                           >  1:5031868/1‑96 (MQ=255)    atGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGCGCTTGTATAGATTTTTAAGTAGAAAActata                                                           >  1:4746804/2‑96 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTCTTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTACGTAGAAAActataag                                                         >  1:6014535/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:339272/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:5403195/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:4211522/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:4065487/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:5787217/1‑94 (MQ=255)      ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActataag                                                         >  1:1887412/1‑94 (MQ=255)         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                                >  1:1984657/1‑100 (MQ=255)                            gtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTaaaa                                >  1:3783862/1‑100 (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                         >  1:121878/1‑98 (MQ=255)                                   tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                         >  1:189483/1‑98 (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)                                    agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                        >  1:328609/3‑98 (MQ=255)                                    agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                        >  1:3402249/3‑98 (MQ=255)                                    aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                        >  1:3791734/1‑100 (MQ=255)                                    aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                        >  1:5063431/1‑100 (MQ=255)                                    aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                        >  1:2917194/1‑100 (MQ=255)                                    aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                        >  1:3105097/1‑100 (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           >  1:4967305/1‑100 (MQ=255)                                                 ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt           >  1:1747726/1‑100 (MQ=255)                                                 ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt           >  1:424797/1‑100 (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          >  1:2783531/1‑100 (MQ=255)                                                  tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa          >  1:1335662/1‑100 (MQ=255)                                                  tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa          >  1:4244771/1‑100 (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)                                                                                              |                                                                   TCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATT  >  NC_007790/1370‑1526

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑