Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,962,266	Δ1 bp	coding (71/531 nt)	rppH ←	RNA pyrophosphohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,962,264	0	C	.	100.0%	134.9 / NA	32	coding (73/531 nt)	rppH	RNA pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (18/14);  total (18/14)

CAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTC  >  NZ_CP009273/2962175‑2962347                                                                                          |                                                                                    cAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGc                                                                                     <  1:61594/90‑1 (MQ=255)   aTTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGcca                                                                                   >  1:190210/1‑89 (MQ=255)   aTTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGcca                                                                                   >  1:366139/1‑89 (MQ=255)      cACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGccacat                                                                                <  2:812163/90‑5 (MQ=255)             cATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGc                                                                        >  1:559995/1‑90 (MQ=255)             cATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGc                                                                        >  2:371911/1‑90 (MQ=255)                 gCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCt                                                                    >  1:336886/1‑90 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCt                                                                          >  2:754070/1‑81 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCt                                                                          <  2:583862/81‑1 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCt                                                                          >  1:583862/1‑81 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCt                                                                          <  1:754070/81‑1 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGc                                                                 >  2:666515/1‑90 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGc                                                                 >  1:497191/1‑90 (MQ=255)                    tGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGc                                                                 >  2:460905/1‑90 (MQ=255)                     gCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCg                                                                <  1:96062/90‑1 (MQ=255)                          gCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTAc                                                           >  1:184740/1‑90 (MQ=255)                          gCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTAc                                                           <  2:190210/90‑1 (MQ=255)                               ttCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATc                                                      >  1:156030/1‑90 (MQ=255)                                    cGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGAt                                                 >  2:223615/1‑90 (MQ=255)                                    cGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGAt                                                 >  2:29817/1‑90 (MQ=255)                                    cGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGAt                                                 >  2:715501/1‑90 (MQ=255)                                           gATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACg                                          >  1:871780/1‑90 (MQ=255)                                                cGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACg                                                   >  1:62177/1‑76 (MQ=255)                                                cGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACg                                                   <  2:62177/76‑1 (MQ=255)                                                  ccTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGc                                   <  1:617938/90‑1 (MQ=255)                                                                   ggAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGtcatca                  >  1:446919/1‑90 (MQ=255)                                                                   ggAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGtcatca                  <  2:329278/90‑1 (MQ=255)                                                                    gAGTGCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaa                 <  2:530663/90‑1 (MQ=255)                                                                        gCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCAc             <  2:497191/90‑1 (MQ=255)                                                                        gCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCAc             >  2:707184/1‑90 (MQ=255)                                                                        gCTGACCAAATCGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCAc             >  1:205843/1‑90 (MQ=255)                                                                                   cGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc  <  1:707073/90‑1 (MQ=255)                                                                                   cGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc  <  2:559995/90‑1 (MQ=255)                                                                                   cGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc  <  2:390959/90‑1 (MQ=255)                                                                                   cGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc  <  1:393860/90‑1 (MQ=255)                                                                                   cGCCGGG‑CCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc  <  1:672153/90‑1 (MQ=255)                                                                                          |                                                                                    CAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTC  >  NZ_CP009273/2962175‑2962347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑