Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,103,871	(A)7→6	intergenic (+71/+78)	BW25113_RS15410 → / ← yghD	tRNA‑Phe/GspM family type II secretion system protein YghD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,103,865	0	A	.	100.0%	113.4 / NA	27	intergenic (+65/+84)	BW25113_RS15410/yghD	tRNA‑Phe/GspM family type II secretion system protein YghD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (9/18);  total (9/18)

ATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT  >  NZ_CP009273/3103782‑3103949                                                                                    |                                                                                     aTTCCGCGTCCGGGCCCCACTAATTCTTAAGACCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                <  2:70547/90‑2 (MQ=255) aTTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                >  2:118741/1‑89 (MQ=255)      gAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCt                                                                          >  1:443120/1‑90 (MQ=255)           cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                     <  2:38421/90‑1 (MQ=255)                  cacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTgg                                                              >  1:708850/1‑90 (MQ=255)                   acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                             <  1:432469/90‑1 (MQ=255)                   acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                             <  2:422011/90‑1 (MQ=255)                      aaTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGa                                                          >  2:113893/1‑90 (MQ=255)                           ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc                                                     >  2:4707/1‑90 (MQ=255)                                 aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               <  1:605000/90‑1 (MQ=255)                                 aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               <  2:401209/90‑1 (MQ=255)                                 aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               <  2:575963/90‑1 (MQ=255)                                   ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             <  1:268943/90‑1 (MQ=255)                                   ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             <  2:125606/90‑1 (MQ=255)                                   ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             <  2:33989/90‑1 (MQ=255)                                    cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                            >  2:87888/1‑90 (MQ=255)                                    cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                            >  2:56113/1‑90 (MQ=255)                                           aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                     <  1:130159/90‑1 (MQ=255)                                                        gCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAt                        <  1:4707/90‑1 (MQ=255)                                                         cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                       <  2:692631/90‑1 (MQ=255)                                                              ggATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGatat                  <  2:708850/90‑1 (MQ=255)                                                                   tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc             <  1:56113/90‑1 (MQ=255)                                                                     aCAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtctc           >  2:342730/1‑90 (MQ=255)                                                                          aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt      <  1:87888/90‑1 (MQ=255)                                                                          aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt      <  1:41155/90‑1 (MQ=255)                                                                           aCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATa     <  1:629190/90‑1 (MQ=255)                                                                              ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             >  1:716016/1‑47 (MQ=255)                                                                              ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             <  2:716016/47‑1 (MQ=255)                                                                              ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt  >  1:199638/1‑90 (MQ=255)                                                                                    |                                                                                     ATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT  >  NZ_CP009273/3103782‑3103949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑