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%	119.7 / NA	35	I305V (ATT→GTT)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/15);  total (20/15)

TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAC  >  NZ_CP009273/2859919‑2860084                                                                                |                                                                                       tactCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca                                                                              <  2:1238422/90‑1 (MQ=255)     cgcgGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGtt                                                                          >  2:35151/1‑90 (MQ=255)         gAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACg                                                                      >  2:20150/1‑90 (MQ=255)           aCAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACggg                                                                    <  2:191546/90‑1 (MQ=255)             aGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTg                                                                  <  2:173514/90‑1 (MQ=255)                 cTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGc                                                              >  2:1233025/1‑90 (MQ=255)                   tCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCa                                                            >  2:668497/1‑90 (MQ=255)                          tCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc                                                     <  2:50789/90‑1 (MQ=255)                           cAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACg                                                    >  2:317870/1‑90 (MQ=255)                             gCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAc                                                  >  2:941500/1‑90 (MQ=255)                              ccccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGAcc                                                 <  2:965137/90‑1 (MQ=255)                                ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTa                                               >  2:1182359/1‑90 (MQ=255)                                ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTa                                               >  1:138319/1‑90 (MQ=255)                                  tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa                                             <  1:601075/90‑1 (MQ=255)                                  tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa                                             >  1:333991/1‑90 (MQ=255)                                   gCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACAt                                            <  2:99871/90‑1 (MQ=255)                                       ttGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTc                                        >  2:274133/1‑90 (MQ=255)                                       ttGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTc                                        >  1:1118678/1‑90 (MQ=255)                                        tGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTcc                                       <  1:317870/90‑1 (MQ=255)                                             gATTTCGCGCAAACGGCGCAGGCCTTCAACCTGGACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAgtgt                                  >  1:928276/1‑90 (MQ=255)                                                 tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGcc                              <  2:1144084/90‑1 (MQ=255)                                                 tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGcc                              >  1:236516/1‑90 (MQ=255)                                                 tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGcc                              <  1:941500/90‑1 (MQ=255)                                                                 ggCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCGCGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCa              >  1:549524/1‑90 (MQ=255)                                                                  gCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCaa             <  2:333991/90‑1 (MQ=255)                                                                      tCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc                                                     >  1:1118592/1‑46 (MQ=255)                                                                      tCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc                                                     <  2:1118592/46‑1 (MQ=255)                                                                      tCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCg         >  1:323452/1‑90 (MQ=255)                                                                      tCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCg         >  1:774746/1‑90 (MQ=255)                                                                      tCAACCTGAACCTGGCGAACACGTTCACGGGGGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCg         >  2:747198/1‑90 (MQ=255)                                                                           cTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCg    >  1:565914/1‑90 (MQ=255)                                                                            tGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGa   >  1:1204/1‑90 (MQ=255)                                                                             gAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAc  <  2:28161/90‑1 (MQ=255)                                                                             gAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAc  <  1:1181442/90‑1 (MQ=255)                                                                             gAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAc  <  2:1118678/90‑1 (MQ=255)                                                                                |                                                                                       TACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGAC  >  NZ_CP009273/2859919‑2860084

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑