Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	658,668	5 bp→GAGCC	intergenic (+233/‑59)	SAUSA300_RS03130 → / → SAUSA300_RS03135	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	658,668	0	T	G	100.0%	17.0 / NA	8	intergenic (+233/‑63)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (5/3);  total (5/3)
*	NC_007793	658,669	0	T	A	100.0%	18.1 / NA	8	intergenic (+234/‑62)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (5/3);  total (5/3)
*	NC_007793	658,670	0	T	G	100.0%	17.1 / NA	8	intergenic (+235/‑61)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (5/3);  total (5/3)
*	NC_007793	658,671	0	T	C	100.0%	16.3 / NA	8	intergenic (+236/‑60)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/3);  total (5/3)
*	NC_007793	658,672	0	T	C	100.0%	15.9 / NA	8	intergenic (+237/‑59)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/3);  total (5/3)

TTTTCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCTTTTTTTTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTGAGAAAG  >  NC_007793/658588‑658739                                                                                 |||||                                                                    ttttCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGt                                                      >  1:2087171/1‑100 (MQ=38) cagccccTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGt                                                      >  1:45378/5‑100 (MQ=255)  tttCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGtt                                                     >  1:4458367/1‑100 (MQ=255)                aTTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGc                                       <  1:1268534/100‑1 (MQ=38)                        ttGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAagtt                               >  1:3966540/1‑100 (MQ=255)                                    tACGCGAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTg                   <  1:1960514/100‑1 (MQ=255)                                      cGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGa                 <  1:1625645/100‑1 (MQ=255)                                                     aaaTGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTGAGAAAg  >  1:4817263/1‑100 (MQ=255)                                                                                 |||||                                                                    TTTTCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCTTTTTTTTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTGAGAAAG  >  NC_007793/658588‑658739

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑