Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,482	0	C	T	78.3%	78.4 / 11.4	46	intergenic (+486/‑97)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (9/1);  new base T (36/0);  total (45/1)
Fisher's exact test for biased strand distribution p-value = 2.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTGTTTATTTT  >  NC_007790/1396‑1580                                                                                          |                                                                                                   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                                                                               >  1:2060975/1‑98 (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                                                                               >  1:189483/1‑98 (MQ=255)         tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATAccctc                                                                               >  1:121878/1‑98 (MQ=255)          agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                                                                              >  1:3402249/3‑98 (MQ=255)          agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGCGTATATA‑AGTTTTGGATAGAAAAAATAT‑ATGATTTA‑CCCCTAAACCTTTAAAATGcccctt                                                                              >  1:328609/3‑98 (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                                                                              >  1:3105097/1‑100 (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                                                                >  1:2783531/1‑100 (MQ=255)                        tGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATa                                                                >  1:4244771/1‑100 (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)                                                                                       accccTAAATCTTTAAAATACCCCCTTAAAATTCAAAATAAAGGAATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTAtt    >  1:4710401/2‑100 (MQ=255)                                                                                         cccTAAATCTTTAAAATACCCCCTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTAtttt  >  1:3067122/1‑100 (MQ=255)                                                                                          |                                                                                                   TGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTGTTTATTTT  >  NC_007790/1396‑1580

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: ‑