Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,087,432	A→G	intergenic (‑82/‑232)	rhaD ← / → rhaS	rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,087,432	0	A	G	100.0%	189.6 / NA	53	intergenic (‑82/‑232)	rhaD/rhaS	rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (30/23);  total (30/23)

CATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGACCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATT  >  NZ_CP009273/4087352‑4087512                                                                                 |                                                                                 cATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt                                                                         <  2:4287/90‑1 (MQ=255)      ggATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTg                                                                    <  1:977036/90‑1 (MQ=255)          ccTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAg                                                                >  2:861879/1‑90 (MQ=255)                 agTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATg                                                         >  2:716741/1‑90 (MQ=255)                   tCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATggg                                                       >  2:852106/1‑90 (MQ=255)                    cGACATATGGTGATCCTGCTGAATTTCATTACGGCCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACa                                                                 >  1:107165/1‑79 (MQ=255)                    cGACATATGGTGATCCTGCTGAATTTCATTACGGCCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACa                                                                 <  2:107165/79‑1 (MQ=255)                    cGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGc                                                      >  2:842469/1‑90 (MQ=255)                     gACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCT‑AAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCa                                                    >  2:1003720/1‑90 (MQ=255)                       cATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCAt                                                   >  1:769654/1‑90 (MQ=255)                         tatGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTg                                                 >  1:311739/1‑90 (MQ=255)                          atGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTgg                                                >  2:203524/1‑90 (MQ=255)                            ggTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCa                                              >  2:849418/1‑90 (MQ=255)                            ggTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCa                                              >  2:688852/1‑90 (MQ=255)                              tGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAc                                            >  2:377319/1‑90 (MQ=255)                              tGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAc                                            >  1:771573/1‑90 (MQ=255)                                aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa                                          >  2:135981/1‑90 (MQ=255)                                aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa                                          <  2:31676/90‑1 (MQ=255)                                aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCAGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa                                          >  2:300316/1‑90 (MQ=255)                                 tCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAcc                                           <  1:922518/88‑1 (MQ=255)                                 tCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAcc                                           >  2:922518/1‑88 (MQ=255)                                   ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt                                                                         >  2:982437/1‑56 (MQ=255)                                   ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt                                                                         <  1:982437/56‑1 (MQ=255)                                   ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAggg                                       >  2:491946/1‑90 (MQ=255)                                    ttctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGa                                      >  1:227241/3‑90 (MQ=255)                                    tgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGa                                      >  2:900733/1‑90 (MQ=255)                                     gctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTAc                                                                      >  2:452506/1‑57 (MQ=255)                                     gctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTAc                                                                      <  1:452506/57‑1 (MQ=255)                                       tgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAg                                   >  2:849523/1‑90 (MQ=255)                                           tttCATTACGACCAGTCT‑AAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGaa                              <  1:1003720/90‑1 (MQ=255)                                             tCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGCTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAAc                             <  2:97324/90‑1 (MQ=255)                                                  aCGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgat                        >  1:330541/1‑90 (MQ=255)                                                    gACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga                      <  1:159798/90‑1 (MQ=255)                                                           cTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTcac               <  1:32645/90‑1 (MQ=255)                                                             aaaaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACaa             <  1:280668/90‑1 (MQ=255)                                                               aaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAAtt           <  1:849418/90‑1 (MQ=255)                                                               aaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAAtt           <  1:688852/90‑1 (MQ=255)                                                                  gcgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGc        <  2:878793/90‑1 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAAt                                                          >  1:441627/1‑39 (MQ=39)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAAt                                                          <  2:441627/39‑1 (MQ=39)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGa                                  >  2:466098/1‑63 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGa                                  <  1:466098/63‑1 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga                      <  1:1035664/75‑1 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga                      >  2:1035664/1‑75 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt       >  1:1014745/1‑90 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt       >  2:967791/1‑90 (MQ=255)                                                                   cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt       >  2:277640/1‑90 (MQ=255)                                                                     ccTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtga                         >  1:169961/1‑70 (MQ=255)                                                                     ccTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtga                         <  2:169961/70‑1 (MQ=255)                                                                       tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt   <  2:588833/90‑1 (MQ=255)                                                                       tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt   <  1:552245/90‑1 (MQ=255)                                                                       tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt   <  1:102044/90‑1 (MQ=255)                                                                        gAATTCGCGGGCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAtt  <  2:769654/90‑1 (MQ=255)                                                                                 |                                                                                 CATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGACCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATT  >  NZ_CP009273/4087352‑4087512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑