Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 1,523,317 G→T 100% pseudogene (1159/2037 nt) rhsE → pseudogene, Rhs family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092731,523,3170GT100.0% 93.3 / NA 35pseudogene (1159/2037 nt)rhsEpseudogene, Rhs family protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (19/16);  total (19/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACTGGTGCGGCTGCTGGACAGGCTGGAGGAAGAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCC  >  CP009273/1523285‑1523461
                                |                                                                                                                                                
aaCTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGCCAGGTGGAGCCGGAATACACACCGGCGCGAAAAGt                               <  2:2363866/148‑1 (MQ=11)
aaCTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGt                               <  1:1139109/148‑1 (MQ=11)
aaCTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGt                               >  1:2675110/1‑148 (MQ=11)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             >  2:1825977/1‑148 (MQ=17)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             <  2:2916323/148‑1 (MQ=17)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             <  2:2915650/148‑1 (MQ=17)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             <  1:281170/148‑1 (MQ=17)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             >  2:1404931/1‑148 (MQ=17)
  cTGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTc                             >  2:1402985/1‑148 (MQ=17)
   tGGTGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACATGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCa                            <  2:3094608/148‑1 (MQ=17)
      tGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCACCTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCAttt                         >  2:2998089/1‑148 (MQ=18)
      tGCGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCAttt                         <  2:2225503/148‑1 (MQ=18)
        cGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCAttttt                       <  2:1313327/148‑1 (MQ=21)
        cGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCAttttt                       <  2:145425/148‑1 (MQ=21)
        cGGCTGCTGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCAttttt                       <  2:147738/148‑1 (MQ=21)
          gctgctGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCACCTGGCCAGACCGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAc                     >  2:1979054/1‑148 (MQ=255)
          gctgctGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGACTACACACCGGCGCGAAAAGTTCATTTTTAc                     >  2:1979055/1‑148 (MQ=25)
          gctgctGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAc                     <  2:1328314/148‑1 (MQ=25)
          gctgctGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAc                     <  2:3180877/148‑1 (MQ=25)
          gctgctGGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAc                     >  2:1784433/1‑148 (MQ=25)
           ctgctgGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAcc                    <  1:1213816/148‑1 (MQ=25)
           ctgctgGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTAcc                    >  2:164413/1‑148 (MQ=25)
            tgctgGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCa                   <  1:2378912/148‑1 (MQ=37)
            tgctgGACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCa                   <  1:1423354/148‑1 (MQ=37)
                 gACAGGCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCg              >  1:765932/1‑148 (MQ=37)
                     ggCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGacca          >  1:1385384/1‑148 (MQ=37)
                     ggCTGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGacca          >  1:1384868/1‑148 (MQ=37)
                        tGGAGGAATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCg       <  2:3011257/148‑1 (MQ=37)
                         ggaggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCgg      >  2:4641/1‑148 (MQ=37)
                          gaggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCggg     >  2:1756993/1‑148 (MQ=37)
                          gaggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCggg     >  2:3342489/1‑148 (MQ=37)
                           aggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCgggg    >  1:3418471/1‑148 (MQ=37)
                           aggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCgggg    >  2:845410/1‑148 (MQ=37)
                            ggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCTACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGc   >  1:943969/1‑148 (MQ=255)
                            ggaATAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGc   >  1:2856860/1‑148 (MQ=38)
                             gaataaATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGcc  >  2:2001733/1‑148 (MQ=38)
                             gaataaATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGcc  >  1:2087787/1‑148 (MQ=38)
                                |                                                                                                                                                
AACTGGTGCGGCTGCTGGACAGGCTGGAGGAAGAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCC  >  CP009273/1523285‑1523461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑