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%	193.8 / NA	43	coding (616/1500 nt)	pitA	inorganic phosphate transporter PitA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/21);  total (22/21)

TGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAAAGGCAT  >  NZ_CP009273/3631531‑3631702                                                                                       |                                                                                      tgcGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAgcgcc                                                                                    <  2:345281/90‑4 (MQ=255)    gTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGtt                                                                                >  1:101136/1‑90 (MQ=255)           cTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcg                                                                         <  1:716942/90‑1 (MQ=255)             ggAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGAcgcg                                                                       >  1:253485/1‑90 (MQ=255)                gCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAt                                                                    <  1:917645/90‑1 (MQ=255)                gCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAt                                                                    <  2:774795/90‑1 (MQ=255)                 cGGCACCAAGAAACGCGCCCGTATCCCCCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                                   <  1:471294/90‑1 (MQ=255)                 cGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTAtt                                                                   >  2:584270/1‑90 (MQ=255)                  ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTg                                                                  >  2:83519/1‑90 (MQ=255)                  ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTg                                                                  >  1:709207/1‑90 (MQ=255)                  ggCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTg                                                                  >  2:656226/1‑90 (MQ=255)                    cACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcg                                                                >  1:168367/1‑90 (MQ=255)                     aCCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                               <  1:453139/90‑1 (MQ=255)                     aCCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                               <  1:425830/90‑1 (MQ=255)                     aCCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                               <  1:242072/90‑1 (MQ=255)                        aaGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGa                                                            >  1:946658/1‑90 (MQ=255)                             aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                                       >  2:621213/1‑90 (MQ=255)                             aCGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCtt                                                       >  2:805578/1‑90 (MQ=255)                                cgcCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTcc                                                    <  2:672126/90‑1 (MQ=255)                                cgcCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTcc                                                    >  1:390721/1‑90 (MQ=255)                                            ccTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtg                                        >  1:97364/1‑90 (MQ=255)                                             cTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtgg                                       <  2:60460/90‑1 (MQ=255)                                              tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                                      <  2:823318/90‑1 (MQ=255)                                              tGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggc                                      <  2:547728/90‑1 (MQ=255)                                               gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                                     >  1:171194/1‑90 (MQ=255)                                               gACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCggcgtggcg                                     >  2:747714/1‑90 (MQ=255)                                                        ggAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCAc                            >  1:845343/1‑90 (MQ=255)                                                         gAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACg                           <  1:869439/90‑1 (MQ=255)                                                         gAGCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACg                           <  1:431642/90‑1 (MQ=255)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                               <  2:348303/52‑1 (MQ=38)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTgcgc                                                               >  1:348303/1‑52 (MQ=38)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                         >  2:108491/1‑90 (MQ=255)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                         >  2:840810/1‑90 (MQ=255)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                         >  1:638691/1‑90 (MQ=255)                                                           gCGTGAAAAGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGgc                         >  2:741116/1‑90 (MQ=255)                                                                aaaaGAAAGACGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGaa                    >  1:805511/1‑90 (MQ=255)                                                                   agaaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa                 <  1:692723/90‑1 (MQ=255)                                                                    gaaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGAt                <  1:741116/90‑1 (MQ=255)                                                                     aaagaCGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATg               <  2:471893/90‑1 (MQ=255)                                                                          cGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa                 <  1:407049/83‑1 (MQ=255)                                                                          cGGCAAGAAAAAG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGa                 >  2:407049/1‑83 (MQ=255)                                                                                 aaaaaG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAAAGGCa   <  2:253485/90‑1 (MQ=255)                                                                                  aaaaG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAAAGGCAt  <  2:821713/90‑1 (MQ=255)                                                                                  aaaaG‑CGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAAAGGCAt  <  2:858031/90‑1 (MQ=255)                                                                                       |                                                                                      TGCGTCGCTACTGGAGCGGCACCAAGAAACGCGCCCGTATCCACCTGACCCCAGCGGAGCGTGAAAAGAAAGACGGCAAGAAAAAGCCGCCGTTCTGGACGCGTATTGCGCTGATCCTTTCCGCTATCGGCGTGGCGTTTTCGCACGGCGCGAACGATGGTCAGAAAGGCAT  >  NZ_CP009273/3631531‑3631702

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: ‑