Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,991,336 T→C pseudogene (852/1137 nt) BW25113_RS14890 ← glycoside hydrolase family 15 protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,991,3360TC90.0% 24.1 / ‑3.0 10pseudogene (852/1137 nt)BW25113_RS14890glycoside hydrolase family 15 protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (4/5);  total (5/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.74e-01

GTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCTTCCATAACATAGAAATT  >  NZ_CP009273/2991254‑2991419
                                                                                  |                                                                                   
gTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAgg                                                                              >  1:329351/1‑90 (MQ=255)
  tCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAGGTc                                                                            <  2:329351/90‑1 (MQ=255)
     ttGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAGGTCAcc                                                                         <  1:515380/90‑1 (MQ=255)
                 tCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAGGTCACCAGTGCAACGGaa                                                             >  1:269697/1‑90 (MQ=255)
                                gagaCAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCgg                                              >  2:262011/1‑90 (MQ=255)
                                                   tcttcGAGAGTAGGTTTGACAAACGTTCCAGCCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTc                           <  1:96016/90‑1 (MQ=255)
                                                            gTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAATGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCtt                  >  1:329339/1‑90 (MQ=255)
                                                            gTAGGTTTGACAAACGTTCCAGCCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCtt                  >  1:103227/1‑90 (MQ=255)
                                                                gTTTGACAAACGTTCCAGCCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCTTCCAt              <  1:492520/90‑1 (MQ=255)
                                                                            ttCCAGCCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCTTCCATAACATAGAAAtt  <  2:73080/90‑1 (MQ=255)
                                                                                  |                                                                                   
GTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAGATGTGTTTAATCGGGCATCTTCTTCCCATGCTCAGGAATCTTCCATAACATAGAAATT  >  NZ_CP009273/2991254‑2991419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑