Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,653,478	C→A	intergenic (+139/‑377)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/small regulatory RNA RyfA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,653,478	0	C	A	100.0%	32.8 / NA	11	intergenic (+139/‑377)	sseA/ryfA	3‑mercaptopyruvate sulfurtransferase/small regulatory RNA RyfA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (3/8);  total (3/8)

GGCCTTTCCAGCAGGTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTCTCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGTATTATCGACACCGGCCCTT  >  NC_000913/2653402‑2653541                                                                             |                                                                ggCCTTTCCAGCAGGTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCtt                                                             <  1:454696/81‑1 (MQ=255)        ccAGCAGGTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTc                                                       <  2:454697/80‑1 (MQ=255)         cagcagGTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCa                                                      <  2:454698/80‑1 (MQ=255)               gTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCaa                                                 >  1:454708/1‑79 (MQ=255)                             cATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAattatt                                  <  2:454699/80‑1 (MQ=255)                             cATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAattatt                                  <  2:454700/80‑1 (MQ=255)                             cATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAattatt                                  <  2:454701/80‑1 (MQ=255)                                         aGGTGCTTCACAGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGt                     <  1:454702/81‑1 (MQ=255)                                                 cacaGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGTATTATCg              <  2:454703/80‑1 (MQ=255)                                                  acaGCAAAACAATACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGTATTATCGa             >  2:454714/1‑80 (MQ=255)                                                            aaTACTCACCAGTAACTATCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGTATTATCGACACCGGCCCtt  >  2:454713/1‑81 (MQ=255)                                                                             |                                                                GGCCTTTCCAGCAGGTTGACTTGTGTTACATGAGCAACGCAGGTGCTTCACAGCAAAACAATACTCACCAGTAACTCTCTTTTTGTCAAGCAAAAGAGAGTAATTATTGTTTATTTAGCGTATTATCGACACCGGCCCTT  >  NC_000913/2653402‑2653541

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑