Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,860,429	T→G	Q161P (CAA→CCA)	rpoS ←	RNA polymerase sigma factor RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,860,429	0	T	G	100.0%	61.5 / NA	19	Q161P (CAA→CCA)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (9/10);  total (9/10)

ACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAA  >  NZ_CP009273/2860358‑2860511                                                                        |                                                                                   aCTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGtt                                                                  >  1:304407/1‑90 (MQ=255)    cACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCaa                                                               <  2:134640/90‑1 (MQ=255)            gTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTgg                                                       >  1:118207/1‑90 (MQ=255)              tCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCg                                                     >  2:213336/1‑90 (MQ=255)                gCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGaa                                                   <  2:28122/90‑1 (MQ=255)                      aaaCGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATccacc                                             <  2:284397/90‑1 (MQ=255)                       aaCGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATccacca                                            <  1:26060/90‑1 (MQ=255)                           ttCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGtt                                        >  2:159815/1‑90 (MQ=255)                             cAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGc                                      >  1:117894/1‑90 (MQ=255)                              aGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCg                                     >  1:248240/1‑90 (MQ=255)                              aGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCg                                     <  2:54337/90‑1 (MQ=255)                                    tttACGATGTGAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGtt                               >  1:151028/1‑90 (MQ=255)                                            gtgAATCGGCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCg                       >  1:29268/1‑90 (MQ=255)                                                   ggCAAACGAATAGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCa                <  1:229289/90‑1 (MQ=255)                                                              aGTACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTc     <  1:107423/90‑1 (MQ=255)                                                                tACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaa   <  2:129533/90‑1 (MQ=255)                                                                tACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaa   <  1:21337/90‑1 (MQ=255)                                                                tACGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaa   <  2:248240/90‑1 (MQ=255)                                                                 aCGGGTTGGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaaa  >  2:137768/1‑90 (MQ=255)                                                                        |                                                                                   ACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAA  >  NZ_CP009273/2860358‑2860511

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑