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%	177.4 / NA	41	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 . (11/30);  total (11/30)

GGTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT  >  NZ_CP009273/3103776‑3103949                                                                                          |                                                                                     ggTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGa                                                                                      <  2:1150777/90‑1 (MQ=255)      gATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaa                                                                                 >  1:372270/1‑90 (MQ=255)       aTTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                <  2:600769/90‑2 (MQ=255)           cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGc                                                                           <  1:700348/90‑1 (MQ=255)           cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGc                                                                           <  2:452943/90‑1 (MQ=255)                ccGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTtata                                                                      <  2:1120030/90‑1 (MQ=255)                 cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                     <  2:912379/90‑1 (MQ=255)                 cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                     <  1:881652/90‑1 (MQ=255)                  gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTACAATAACCTTCACG‑AAAAAATTAGCTTATaaa                                                                    >  1:1017093/1‑90 (MQ=255)                       ccacTAATTCTTAAGACCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTg                                                               <  1:657570/90‑1 (MQ=255)                         acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                             <  2:90042/90‑1 (MQ=255)                         acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                             <  2:133722/90‑1 (MQ=255)                              ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGTCAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAAt                                                        <  2:593893/90‑1 (MQ=255)                              ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAAt                                                        <  2:763151/90‑1 (MQ=255)                               tCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAAtt                                                       <  1:164706/90‑1 (MQ=255)                                 ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc                                                     >  2:237863/1‑90 (MQ=255)                                 ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc                                                     >  1:891083/1‑90 (MQ=255)                                       aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               <  2:186541/90‑1 (MQ=255)                                       aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               >  2:963949/1‑90 (MQ=255)                                        cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               >  1:1109138/1‑89 (MQ=255)                                        cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                               <  2:1109138/89‑1 (MQ=255)                                         ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                             <  2:145620/90‑1 (MQ=255)                                          cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                <  2:337014/55‑2 (MQ=255)                                          cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                >  1:337014/1‑54 (MQ=255)                                          cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                            >  1:1001848/1‑90 (MQ=255)                                          cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                            >  2:209947/1‑90 (MQ=255)                                               acaAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTaa                                       >  2:553740/1‑90 (MQ=255)                                                 aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                     <  1:89004/90‑1 (MQ=255)                                                 aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                     <  2:480348/90‑1 (MQ=255)                                                    gCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACgaga                                  <  1:209947/90‑1 (MQ=255)                                                      gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt                                <  2:399091/90‑1 (MQ=255)                                                                  ttGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGat                    <  1:1136734/90‑1 (MQ=255)                                                                        cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt              <  2:22097/90‑1 (MQ=255)                                                                        cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt              <  2:372270/90‑1 (MQ=255)                                                                         tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTCCTCTCGCCCCGTTAACGAGAGTAATTTTATTGATATTAAtc             <  1:733770/90‑1 (MQ=255)                                                                         tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc             <  1:362120/90‑1 (MQ=255)                                                                         tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc             <  1:627006/90‑1 (MQ=255)                                                                         tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc             <  1:910320/90‑1 (MQ=255)                                                                          gACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtct            <  1:98566/90‑1 (MQ=255)                                                                              aTAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTg        <  1:905224/90‑1 (MQ=255)                                                                               tAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGa       >  1:937439/1‑90 (MQ=255)                                                                                aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt      <  1:1191944/90‑1 (MQ=255)                                                                                aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt      <  1:976487/90‑1 (MQ=255)                                                                                aaCCTTCACG‑AAAAAATTAACTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt      <  1:721256/90‑1 (MQ=255)                                                                                    ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt  >  2:329215/1‑90 (MQ=255)                                                                                    ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt  >  2:101084/1‑90 (MQ=255)                                                                                          |                                                                                     GGTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT  >  NZ_CP009273/3103776‑3103949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑