Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,502	0	C	T	66.7%	27.9 / 14.2	31	intergenic (+506/‑77)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (8/2);  new base T (18/2);  total (27/4)
Fisher's exact test for biased strand distribution p-value = 5.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTGTTTATTTTGAATAAAAACACAGTGTT  >  NC_007790/1405‑1598                                                                                                     |                                                                                                 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                                                                                                >  1:2917194/1‑100 (MQ=255) aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCctct                                                                                                >  1:5063431/1‑100 (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                                                                                   >  1:424797/1‑100 (MQ=255)              ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                                                                   >  1:4967305/1‑100 (MQ=255)              ttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAAt                                                                                   >  1:1747726/1‑100 (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                                                                                 >  1:4199925/1‑100 (MQ=255)                ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                                                                 >  1:4299006/1‑100 (MQ=255)                ggCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TAGAAAACTAT‑AAGATTTA‑CCTCTAAATCTTTAAAATACCCTCTTAAAATTCAAAATaa                                                                                 >  1:4658108/1‑100 (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)                                                                                 tcTAAATCTTTAAAATACCCTCTTAAAATTCAAAATAAAGGTGTTTATAATTTGAATAAGTCCTGAGATAAAGTTTTTT‑‑AAAAGGAGTGGTT‑TTTTGaag                <  1:5393523/99‑2 (MQ=255)                                                                                       tcTTTAAAATACCCTCTTAAAATTCAAAATAAAGGTGTTTATAATTTGAATAAGTCCTGAGATAAAGTTTTTT‑‑AAAAGGAGTGGTT‑TTTTGaagaggttt          <  1:3011904/99‑8 (MQ=255)                                                                                               aTACCCCCTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTATTTTGAATAAAGACACAgt     >  1:3990512/1‑100 (MQ=255)                                                                                                 aCCCCCTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTATTTTGAATAAAGACACAgtgt   <  1:5902710/100‑1 (MQ=255)                                                                                                  cccccTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTATTTTGAATAAAGACACAGTGtt  <  1:5039293/100‑1 (MQ=255)                                                                                                  cccccTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTATTTTGAATAAAGACACAGTGtt  <  1:2420925/100‑1 (MQ=255)                                                                                                  cccccTTAAAATTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTCTTTATTTTGAATAAAGACACAGTGtt  <  1:3132748/100‑1 (MQ=255)                                                                                                     |                                                                                                 ACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT‑ATGA‑TAC‑CCCCTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTATTTATAATTTGAGTAAGTCTTGTGATAAAGTTTTTTAAAAAAGGAGTGTTTATTTTGAATAAAAACACAGTGTT  >  NC_007790/1405‑1598

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: ‑