Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,505,986	T→C	intergenic (‑283/+7)	BW25113_RS17530 ← / ← trpS	GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,505,986	0	T	C	100.0%	64.5 / NA	21	intergenic (‑283/+7)	BW25113_RS17530/trpS	GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/12);  total (9/12)

ATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGC  >  NZ_CP009273/3505912‑3506057                                                                           |                                                                        atGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCtt                                                          >  1:109451/1‑90 (MQ=255) atGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCtt                                                          >  1:199285/1‑90 (MQ=255)  tgtgCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc                                                         <  2:245840/90‑1 (MQ=255)             ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCg                                                        <  1:207797/80‑1 (MQ=255)             ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCg                                                        >  2:207797/1‑80 (MQ=255)                  ggCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCg                                         <  1:42343/90‑1 (MQ=255)                    ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt                                       >  1:219456/1‑90 (MQ=255)                    ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt                                       >  2:400704/1‑90 (MQ=255)                           aGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGGGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTaca                                >  2:422488/1‑90 (MQ=255)                           aGGCGTCCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTaca                                <  1:51444/90‑1 (MQ=255)                                 tCACGCCGCATCCGGCATGAACAAAGCGCAATTTACCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt                          >  1:272857/1‑90 (MQ=255)                                      ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACGGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc                     <  1:198806/90‑1 (MQ=255)                                      ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc                     <  1:333154/90‑1 (MQ=255)                                      ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc                     <  2:49270/90‑1 (MQ=255)                                      ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc                     <  2:111812/90‑1 (MQ=255)                                      ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc                     <  2:272857/90‑1 (MQ=255)                                            ccGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACgg               <  2:7910/90‑1 (MQ=255)                                                   gAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCg                                         <  2:1096/57‑1 (MQ=255)                                                   gAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCg                                         >  1:1096/1‑57 (MQ=255)                                                   gAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGt        >  2:441556/1‑90 (MQ=255)                                                         aGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTgcgcgc  <  1:427492/90‑1 (MQ=255)                                                                           |                                                                        ATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGC  >  NZ_CP009273/3505912‑3506057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑