Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	1,478	2 bp→TA	intergenic (+482/‑100)	SAUSA300_RS14705 → / → SAUSA300_RS14710	replication protein/membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,478	0	A	T	100.0%	52.7 / NA	19	intergenic (+482/‑101)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (18/1);  total (18/1)
*	NC_007790	1,479	0	C	A	89.5%	45.3 / ‑0.3	19	intergenic (+483/‑100)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (17/0);  minor base T (1/1);  total (18/1)
Fisher's exact test for biased strand distribution p-value = 1.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

TTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑C‑CCC‑CTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTAT  >  NC_007790/1395‑1525                                                                                      |||                                                 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)                                                                                      |||                                                 TTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑C‑CCC‑CTAAACCTTTAAAATACCCCCTTAAAACTCAAAATAAAGGTAT  >  NC_007790/1395‑1525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑