Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,631,615	(A)5→4	coding (614/1500 nt)	pitA →	inorganic phosphate transporter PitA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,631,611	0	A	.	100.0%	101.6 / NA	24	coding (610/1500 nt)	pitA	inorganic phosphate transporter PitA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (15/9);  total (15/9)

CTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAG  >  NZ_CP009273/3631541‑3631694                                                                       |                                                                                    cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                 <  2:259045/90‑1 (MQ=255)      gCGGCACCAAGAAACGCGCCCGTATCCCCCTGCCCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTAt                                                            <  1:453158/90‑1 (MQ=255)      gCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTAt                                                            <  2:85503/90‑1 (MQ=255)       cGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTAtt                                                           >  2:136426/1‑90 (MQ=255)        ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                 <  1:178153/83‑1 (MQ=255)        ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                 >  2:178153/1‑83 (MQ=255)        ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTg                                                          >  2:142191/1‑90 (MQ=255)                 aaaCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATcc                                                 <  1:136426/90‑1 (MQ=255)                   aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                               >  2:575897/1‑90 (MQ=255)                               ccACCTGCCCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggc                                   <  1:156550/90‑1 (MQ=255)                                    tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                              >  1:216605/1‑90 (MQ=255)                                     gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                             >  1:561033/1‑90 (MQ=255)                                     gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                             >  1:55904/1‑90 (MQ=255)                                      aCCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcgt                            >  2:10128/1‑90 (MQ=255)                                         ccAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGtttt                         >  2:486335/1‑90 (MQ=255)                                          cAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTc                        >  1:581600/1‑90 (MQ=255)                                                 gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                 >  1:551532/1‑90 (MQ=255)                                                 gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                 >  2:28403/1‑90 (MQ=255)                                                   gTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgcgc               >  2:367385/1‑90 (MQ=255)                                                           aaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATg       >  2:398626/1‑90 (MQ=255)                                                           aaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATg       <  2:581600/90‑1 (MQ=255)                                                              gaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTc    <  1:292327/90‑1 (MQ=255)                                                              gaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTc    <  1:28403/90‑1 (MQ=255)                                                                cGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAg  >  1:282364/1‑90 (MQ=255)                                                                       |                                                                                    CTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAG  >  NZ_CP009273/3631541‑3631694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑