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%	16.6 / NA	9	intergenic (+233/‑63)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (4/5);  total (4/5)
*	NC_007793	658,669	0	T	A	100.0%	20.2 / NA	9	intergenic (+234/‑62)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (4/5);  total (4/5)
*	NC_007793	658,670	0	T	G	100.0%	18.5 / NA	9	intergenic (+235/‑61)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (4/5);  total (4/5)
*	NC_007793	658,671	0	T	C	100.0%	20.1 / NA	9	intergenic (+236/‑60)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/5);  total (4/5)
*	NC_007793	658,672	0	T	C	100.0%	19.9 / NA	9	intergenic (+237/‑59)	SAUSA300_RS03130/SAUSA300_RS03135	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/5);  total (4/5)

TCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCTTTTTTTTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTGAGA  >  NC_007793/658591‑658736                                                                              |||||                                                                 ccccTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGtttt                                                >  1:1465713/2‑100 (MQ=37)  cccTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGttttt                                               >  1:1933264/1‑100 (MQ=37)   ccTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGtttttt                                              >  1:4090562/1‑100 (MQ=37)             aTTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGc                                    <  1:5513398/100‑1 (MQ=38)                ggTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAgg                                 <  1:2042251/100‑1 (MQ=38)                                  aCGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTgg               >  1:1098251/1‑100 (MQ=255)                                            tAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTg     <  1:4545040/100‑1 (MQ=255)                                            tAGCGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTg     <  1:951304/100‑1 (MQ=255)                                               cGAAAATGAATTTTAAAGGTTAAATATAGTCGAGCCTGTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTgaga  <  1:1971843/100‑1 (MQ=255)                                                                              |||||                                                                 TCCCTATGATTAATTGGTTTTTGCCCAAAAAATACGCAAAAATTAGCGAAAATGAATTTTAAAGGTTAAATATAGTCTTTTTTTTTAAAAATAATGTTTTTTGGCCGGTTGCAGGAAGTTCAGTTCTATTTGGAATTATATTGAGA  >  NC_007793/658591‑658736

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑