Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,631,618	Δ1 bp	coding (617/1500 nt)	pitA →	inorganic phosphate transporter PitA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,631,617	0	C	.	100.0%	147.5 / NA	33	coding (616/1500 nt)	pitA	inorganic phosphate transporter PitA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (18/15);  total (18/15)

CTGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGA  >  NZ_CP009273/3631530‑3631687                                                                                        |                                                                       ctgcGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAgcgc                                                                      <  2:377110/90‑3 (MQ=255)         cTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTgg                                                             <  2:384234/90‑1 (MQ=255)         cTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTgg                                                             <  2:174720/90‑1 (MQ=255)            cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcg                                                          <  2:745429/90‑1 (MQ=255)            cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcg                                                          <  1:100826/90‑1 (MQ=255)                  cGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                    <  1:529366/90‑1 (MQ=255)                   ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTg                                                   >  1:12998/1‑90 (MQ=255)                   ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTg                                                   >  1:332705/1‑90 (MQ=255)                      aCCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                <  2:767477/90‑1 (MQ=255)                        cAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTg                                              >  2:115173/1‑90 (MQ=255)                        cAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTg                                              >  1:723195/1‑90 (MQ=255)                              aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                    <  1:178876/78‑1 (MQ=255)                              aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                    >  2:178876/1‑78 (MQ=255)                                            aCCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgt                          <  2:13648/90‑1 (MQ=255)                                             ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcg                                                          <  1:227175/57‑1 (MQ=255)                                             ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcg                                                          >  2:227175/1‑57 (MQ=255)                                             ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                         >  1:638832/1‑90 (MQ=255)                                             ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                         >  1:521633/1‑90 (MQ=255)                                                gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                    >  2:677372/1‑60 (MQ=255)                                                gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                    <  1:677372/60‑1 (MQ=255)                                                gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                      >  1:502657/1‑90 (MQ=255)                                                     cAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTc                 >  1:552773/1‑90 (MQ=255)                                                     cAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTc                 >  1:259589/1‑90 (MQ=255)                                                      aGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCg                >  2:24102/1‑90 (MQ=255)                                                         ggAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCAc             <  2:723195/90‑1 (MQ=255)                                                         ggAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCAc             <  2:657440/90‑1 (MQ=255)                                                            gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc          >  1:217973/1‑90 (MQ=255)                                                            gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc          >  2:78485/1‑90 (MQ=255)                                                            gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc          >  2:580563/1‑90 (MQ=255)                                                              gTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgcgc        <  1:644557/90‑1 (MQ=255)                                                              gTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGGTTTCGCACGgcgc        >  2:673180/1‑90 (MQ=255)                                                                    agaaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa  <  1:24102/90‑1 (MQ=255)                                                                      aaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa  <  2:555538/88‑1 (MQ=255)                                                                      aaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa  >  1:555538/1‑88 (MQ=255)                                                                                        |                                                                       CTGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGA  >  NZ_CP009273/3631530‑3631687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑