Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	520,419	A→T	H568L (CAC→CTC)	rhsD →	rhs element protein RhsD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	520,419	0	A	T	100.0%	105.5 / NA	29	H568L (CAC→CTC)	rhsD	rhs element protein RhsD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (15/14);  total (15/14)

GCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCG  >  NZ_CP009273/520332‑520506                                                                                        |                                                                                        gCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCcg                                                                                      >  2:443485/1‑91 (MQ=255)       ggCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGa                                                                                <  1:608152/91‑1 (MQ=255)            ttGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCa                                                                           >  2:373589/1‑91 (MQ=255)             tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  2:367906/91‑1 (MQ=255)             tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  1:284024/91‑1 (MQ=255)             tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  1:541107/91‑1 (MQ=255)                tGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAg                                                                       <  1:270025/91‑1 (MQ=255)                     ttCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCttt                                                                  >  1:253711/1‑91 (MQ=255)                       cACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTAc                                                                >  1:347745/1‑91 (MQ=255)                              tGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCt                                                         <  2:856145/91‑1 (MQ=255)                              tGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCt                                                         >  2:85375/1‑91 (MQ=255)                               gCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTa                                                        >  2:411379/1‑91 (MQ=255)                                cTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTAt                                                       >  2:43779/1‑91 (MQ=255)                                 tCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATg                                                      <  2:66849/91‑1 (MQ=255)                                           aGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTgg                                            <  1:555639/91‑1 (MQ=255)                                              cccGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCg                                         >  2:266197/1‑91 (MQ=255)                                                 gTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGtt                                      >  1:697196/1‑91 (MQ=255)                                                  ttATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTa                                     <  1:85375/91‑1 (MQ=255)                                                      gAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCt                                 <  1:111074/91‑1 (MQ=255)                                                         tACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCgg                              <  2:719753/91‑1 (MQ=255)                                                          aCGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGt                             >  1:191080/1‑91 (MQ=255)                                                           cGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTg                            >  2:29205/1‑91 (MQ=255)                                                           cGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTg                            >  1:737564/1‑91 (MQ=255)                                                             aCCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAACAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGaa                          <  1:663686/91‑1 (MQ=255)                                                                gCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGa                       >  1:86251/1‑91 (MQ=255)                                                                          gATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGc             >  2:123292/1‑91 (MQ=255)                                                                          gATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGc             <  2:697196/91‑1 (MQ=255)                                                                               cggcggTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGa        >  1:868924/1‑91 (MQ=255)                                                                                   ggTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcg    <  1:29205/91‑1 (MQ=255)                                                                                     tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:798752/91‑1 (MQ=255)                                                                                     tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:443485/91‑1 (MQ=255)                                                                                     tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  2:799/91‑1 (MQ=255)                                                                                     tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:116288/91‑1 (MQ=255)                                                                                        |                                                                                        GCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCG  >  NZ_CP009273/520332‑520506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑