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%	211.9 / NA	49	coding (610/1500 nt)	pitA	inorganic phosphate transporter PitA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (25/24);  total (25/24)

CTTGCTGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAA  >  NZ_CP009273/3631526‑3631696                                                                                      |                                                                                      cTTGCTGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCGAGaaaag                                                                                   >  1:282591/1‑89 (MQ=255)     ctgcGTCGCTACTGGAGCGGCACCAAGAACCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTAAAAAGAAAGACGGCAAG‑AAAAgccgc                                                                              <  1:542488/90‑1 (MQ=255)     ctgcGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAgccgc                                                                              <  2:319772/90‑1 (MQ=255)     ctgcGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAgccgc                                                                              <  2:470129/90‑1 (MQ=255)         gTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGtt                                                                          >  1:628241/1‑90 (MQ=255)               aCTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAc                                                                    <  2:983976/90‑1 (MQ=255)                cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                   <  2:632967/90‑1 (MQ=255)                cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                   <  2:887820/90‑1 (MQ=255)                cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                   <  2:462791/90‑1 (MQ=255)                cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                   <  1:63125/90‑1 (MQ=255)                cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGAcg                                                                   <  1:721889/90‑1 (MQ=255)                    aGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTa                                                               >  1:179362/1‑90 (MQ=255)                    aGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTa                                                               >  1:699971/1‑90 (MQ=255)                       ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTg                                                            >  2:111373/1‑90 (MQ=255)                       ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTg                                                            >  1:785973/1‑90 (MQ=255)                         cACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTgcg                                                          >  1:907121/1‑90 (MQ=255)                            cAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTg                                                       >  2:977990/1‑90 (MQ=255)                             aaGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGa                                                      <  1:73662/90‑1 (MQ=255)                                  aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                                 >  2:766025/1‑90 (MQ=255)                                  aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                                 >  2:390972/1‑90 (MQ=255)                                  aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                                 >  2:139338/1‑90 (MQ=255)                                     cgcCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTcc                                              <  2:616261/90‑1 (MQ=255)                                      gcCCGTATCCACCTGACCCCAGCGGCGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCg                                             >  1:501408/1‑90 (MQ=255)                                      gcCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCg                                             >  2:879279/1‑90 (MQ=255)                                                 ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                                  >  1:411288/1‑90 (MQ=255)                                                 ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                                  >  2:242280/1‑90 (MQ=255)                                                 ccTGACCCCAGCGGAGCGTGAAAAAAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                                  <  1:595336/90‑1 (MQ=255)                                                   tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                                >  1:752413/1‑90 (MQ=255)                                                   tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                                >  2:237766/1‑90 (MQ=255)                                                   tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                                <  2:569983/90‑1 (MQ=255)                                                    gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                               >  1:803417/1‑90 (MQ=255)                                                      ccccAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAgccgc                                                                              >  1:657528/1‑41 (MQ=39)                                                      ccccAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAgccgc                                                                              <  2:657528/41‑1 (MQ=39)                                                      ccccAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGtt                             >  2:848504/1‑90 (MQ=255)                                                         cAGCGGAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTc                          >  2:837142/1‑90 (MQ=255)                                                             ggAGGGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCAc                      <  1:925317/90‑1 (MQ=255)                                                             ggAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCAc                      <  1:861475/90‑1 (MQ=255)                                                              gAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACg                     <  1:390972/90‑1 (MQ=255)                                                              gAGCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACg                     >  1:464967/1‑90 (MQ=255)                                                                gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                   >  2:966274/1‑90 (MQ=255)                                                                gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                   >  2:539822/1‑90 (MQ=255)                                                                gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                   >  2:882873/1‑90 (MQ=255)                                                                gCGTGAAAAGAAAGACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                   >  2:746226/1‑90 (MQ=255)                                                                      aaagaaagACGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAAc             <  1:241989/90‑1 (MQ=255)                                                                        agaaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa           <  1:68200/90‑1 (MQ=255)                                                                        agaaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa           <  2:277434/90‑1 (MQ=255)                                                                        agaaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa           <  2:464967/90‑1 (MQ=255)                                                                        agaaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa           <  1:651757/90‑1 (MQ=255)                                                                         gaaagaCGGCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGAt          <  2:787730/90‑1 (MQ=255)                                                                                 gCAAG‑AAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGaa  <  1:549323/90‑1 (MQ=255)                                                                                      |                                                                                      CTTGCTGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAA  >  NZ_CP009273/3631526‑3631696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑