Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,859,998	T→C	I305V (ATT→GTT)	rpoS ←	RNA polymerase sigma factor RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,859,998	0	T	C	100.0%	40.1 / NA	13	I305V (ATT→GTT)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/8);  total (5/8)

TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAA  >  NZ_CP009273/2859919‑2860074                                                                                |                                                                             tactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca                                                                    <  1:257616/90‑1 (MQ=255)   ctCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACg                                                                  >  2:401342/1‑90 (MQ=255)                        atTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTc                                             >  1:46865/1‑90 (MQ=255)                            aGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGa                                         <  2:402570/90‑1 (MQ=255)                             gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAc                                        >  1:209531/1‑90 (MQ=255)                              ccccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAcc                                       <  1:216766/90‑1 (MQ=255)                                ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca                                                                    >  1:389517/1‑59 (MQ=255)                                ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca                                                                    <  2:389517/59‑1 (MQ=255)                                  tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa                                   >  1:112142/1‑90 (MQ=255)                                  tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa                                   <  1:40177/90‑1 (MQ=255)                                          cAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAg                           <  2:209531/90‑1 (MQ=255)                                                        aaCGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGt             <  1:273976/90‑1 (MQ=255)                                                                   ccTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATATTCCAGTGTTGCCGCTTCGTACCCCAGCaaa  <  2:309293/90‑1 (MQ=255)                                                                                |                                                                             TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAA  >  NZ_CP009273/2859919‑2860074

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑