Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,632,157	A→T	I386F (ATC→TTC)	pitA →	inorganic phosphate transporter PitA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,632,157	0	A	T	100.0%	171.5 / NA	45	I386F (ATC→TTC)	pitA	inorganic phosphate transporter PitA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (30/15);  total (30/15)

TGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGATCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGAGAAAATCGGT  >  NZ_CP009273/3632071‑3632243                                                                                       |                                                                                       tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  1:1010778/1‑90 (MQ=255) tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  1:908086/1‑90 (MQ=255) tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  1:499786/1‑90 (MQ=255) tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  2:132222/1‑90 (MQ=255) tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  1:437988/1‑90 (MQ=255) tGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGttca                                                                                     >  1:375914/1‑90 (MQ=255)           gAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGt                                                                           <  2:819794/90‑1 (MQ=255)           gAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGt                                                                           >  2:133232/1‑90 (MQ=255)           gAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGt                                                                           >  2:846303/1‑90 (MQ=255)           gAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGCATGCACCGGTGTGGTTCATCATGGCGGt                                                                           >  2:653888/1‑90 (MQ=255)                cTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGTCATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCgcgc                                                                      <  1:698150/90‑1 (MQ=255)                cTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCgcgc                                                                      <  2:319966/90‑1 (MQ=255)                cTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCgcgc                                                                      <  2:1010778/90‑1 (MQ=255)                 tGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGGGTGGTTCATCATGGCGGTcgcggt                                                                     >  1:622448/1‑88 (MQ=255)                  gACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTg                                                                    >  1:320586/1‑90 (MQ=255)                       tCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGtt                                                               >  1:167852/1‑90 (MQ=255)                        cAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTa                                                              <  1:92777/90‑1 (MQ=255)                              cTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATc                                                        <  2:800989/90‑1 (MQ=255)                              cTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATc                                                        <  2:953353/90‑1 (MQ=255)                                gTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCgcgc                                                                      <  2:99596/74‑1 (MQ=255)                                gTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCgcgc                                                                      >  1:99596/1‑74 (MQ=255)                                  tGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTa                                                    >  1:128921/1‑90 (MQ=255)                                         aCTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACgatgat                                             <  1:263675/90‑1 (MQ=255)                                          cTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGAtt                                            >  2:355896/1‑90 (MQ=255)                                                 ccGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATtggctggc                                     >  2:456111/1‑90 (MQ=255)                                                    aCATGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGcc                                  >  1:824839/1‑90 (MQ=255)                                                       tGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCgtg                               <  1:744712/90‑1 (MQ=255)                                                       tGCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCgtg                               <  1:456111/90‑1 (MQ=255)                                                        gCTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCgtgt                              >  1:167133/1‑90 (MQ=255)                                                         cTTAGCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGCGAGGTGTCGGTACGGTTTTTTGCTGGCGCCGggtg                             >  2:646472/1‑90 (MQ=255)                                                             gCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCaa                         <  2:414003/90‑1 (MQ=255)                                                             gCACCATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCaa                         <  2:524726/90‑1 (MQ=255)                                                                 cATCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGGTAGGTATCGGGACGATGATTGGCTGGGGCCGGGGGGGAACGAc                     >  2:108447/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  1:338534/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  1:369948/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  2:360783/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  1:844930/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  1:212933/1‑90 (MQ=255)                                                                  aTCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACt                    >  1:172893/1‑90 (MQ=255)                                                                   tCGAGTATGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGGACGATGATTGGCTGGGGCCGGGGTGCAACGACTa                   >  1:988436/1‑90 (MQ=25)                                                                         aTGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGGACGATGATTGGCTGGCGCCGTGGGGCAACGACTATCgggg             >  2:83012/1‑88 (MQ=37)                                                                          tGCACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGGGCCGTGTGGCAACGACTATCGGTga            >  2:836858/1‑90 (MQ=255)                                                                            cACCGGTGTGGTTCATCATGGCGGTCGCGCTGGCGGTAGGTATCGGGACGATGATTGGCTGGCGCCGGGGGGCAACGACCATCGGTgaga          >  2:475022/1‑90 (MQ=21)                                                                               cGGTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGAGaaaa       <  2:471356/90‑1 (MQ=255)                                                                                ggTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGAGAAAAt      >  1:157685/1‑90 (MQ=255)                                                                                ggTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGGGGCAACGGCTATCGGTGAGAAAAt      >  1:137359/1‑90 (MQ=255)                                                                                ggTGTGGTTCATCATGGCGGTCGCGCTGGCGTTAGGGATCGGGACGATGATTGGCTGGCGCCGGGTGGCAACGACTATCGGTGAGGAAAt      >  2:177052/1‑90 (MQ=255)                                                                                ggTGTGGTTCATCATGGCGGTCGCGCTGGCGGTAGGTATTGGTAAGCTGATTGGGTGGGGCCGTGTGGCAACGACTATCGGTGAGAAAAt      >  2:696018/1‑90 (MQ=255)                                                                                 gtgtGGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGGGAAAATc     >  1:972290/1‑90 (MQ=255)                                                                                 gtgtGGTTCATCATGGCGGTCGCGCTGGCGGTAGGTATCGGTACGATGATTGGCTGGCGCCGGGTGGGCACGACTATCGGTGAGAAAATc     >  2:1036997/1‑90 (MQ=25)                                                                                    tgGTTCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGAGAAAATCGGt  <  1:601788/90‑1 (MQ=255)                                                                                       |                                                                                       TGCCTGGCGTGAGTGCTGACGATCAGCGCCTGTTGAAGAAACTGAAGTCCGACATGCTTAGCACCATCGAGTATGCACCGGTGTGGATCATCATGGCGGTCGCGCTGGCGTTAGGTATCGGTACGATGATTGGCTGGCGCCGTGTGGCAACGACTATCGGTGAGAAAATCGGT  >  NZ_CP009273/3632071‑3632243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑