Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA3,548,5730TC28.2% 57.6 / 14.2 39T500A (ACC→GCC) malQ4‑alpha‑glucanotransferase (amylomaltase)
Reads supporting (aligned to +/- strand):  ref base T (14/14);  new base C (0/11);  total (14/25)
Fisher's exact test for biased strand distribution p-value = 3.03e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATC  >  NC_000913_3_pae_tpiA/3548433‑3548715
                                                                                                                                            |                                                                                                                                              
tgtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGAt                                                                                                                                        <  1:205275/149‑1 (MQ=255)
 gtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                                       <  1:401626/149‑1 (MQ=255)
 ctccccgcAACCGCCAACCACTTCACCGGTTACCCTCTCGGTGCACGGAACGTCCTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGCACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                                       <  2:3261/145‑1 (MQ=255)
  tCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTGTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCt                                                                                                                                      >  2:173614/1‑149 (MQ=255)
    gccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTc                                                                                                                                    >  1:234673/1‑149 (MQ=255)
     ccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCa                                                                                                                                   >  2:324935/1‑149 (MQ=255)
                 ttgtctgcgctggatacgctttcggtgcacggaacgtcttctcgtggtcgttttcgaaatagagtactttgtaagagtacaccccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATa                                                                                                                       <  2:148554‑M2/26‑1 (MQ=255)
                   gACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACa                                                                                                                     <  1:324935/149‑1 (MQ=255)
                    aCTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCGCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAg                                                                                                                    <  1:252427/149‑1 (MQ=255)
                          ttggatacgcattctgtgcacggaacgtcttctcgtggtcgttttcgaaatagatcactttgtaagagtacacaccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGa                                                                                                              <  2:119792‑M2/35‑1 (MQ=255)
                           tggatacgctctcggtgcacggaacgtcttctcgtggtcgttttcgaaatagagcactttgtaagagtacacaccgctgctgcgcagcttttttattataactatacggacacCACCGAGATCTACACCAATCACCATACAGCGATGAc                                                                                                             <  2:152735‑M2/36‑1 (MQ=255)
                           cGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCCCCTTACACCGATgcc                                                                                                             >  2:31634/1‑147 (MQ=255)
                                       cGGTGCATGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGa                                                                                                 <  1:504344/149‑1 (MQ=255)
                                          tGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATGTTCACCAGTCACCATACAGCGATGACGTTTACTTTCGGGTg                                                                                              >  1:30105/1‑149 (MQ=255)
                                             acgtaacttcttctcgtggtcgtttgtgaaatagagcactttgtaagagtacgcaccgctgctgcgcagttttttttttttaatgatccggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCa                                                                                           <  2:355105‑M2/54‑1 (MQ=255)
                                                    gTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCga                                                                                    <  1:312609/149‑1 (MQ=255)
                                                            gtggtcgttttggaaatagtggactgtgtaagagtacacaccgctgctgcgcagctttttttttttaatgatccggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGat                                                                            <  2:431370‑M2/69‑1 (MQ=255)
                                                              ggtcgttttcgaaatagcgcactttgtaagagtacacaccgctgctgcgtagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatca                                                                          <  2:369018‑M2/71‑1 (MQ=255)
                                                               gTCGCTTTCGAAATAGAGCACTTTGCAAGAGGACACACCGCTGCGGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTCCACCAACCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcat                                                                         <  1:225422/149‑1 (MQ=255)
                                                                tCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcatc                                                                        >  2:398965/1‑149 (MQ=255)
                                                                  gTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGACAGCAGCTCATCCa                                                                      >  1:196171/1‑149 (MQ=255)
                                                                     ttggaaatagagcactttttacgagtacacaccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCg                                                                   <  2:430582‑M2/78‑1 (MQ=255)
                                                                              gagCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCAACAATCATAACACCCCTATTACCTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          <  2:234673/149‑1 (MQ=255)
                                                                                        tAAGAGTACACATCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGcc                                                <  1:2758/149‑1 (MQ=255)
                                                                                        aagtagtacacaccggtggtgtgtagttttttttttttaatgattgggcgggCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGcc                                                <  2:74902‑M2/97‑1 (MQ=255)
                                                                                             gTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGAt                                           <  1:398965/149‑1 (MQ=255)
                                                                                              tacacaccgctgctgcgcagcttacttactttcatgacacggacacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATc                                          <  2:340384‑M2/103‑1 (MQ=255)
                                                                                              tACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATc                                          <  1:212767/149‑1 (MQ=255)
                                                                                               acacacCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCt                                         >  2:118891/1‑149 (MQ=255)
                                                                                                  cccgctgcctacgtagctttttttttttaatgaccgggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGcc                                      <  2:4228‑M2/107‑1 (MQ=255)
                                                                                                     cGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCTAGTGCCAGAACCGAGAGCAGATCATCCACCGGATAGTGCACATACGCGCCCTGATCTGCCGtc                                   >  2:206208/1‑149 (MQ=255)
                                                                                                               gcgcttatcttttttaattatcgggcggcCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACg                         <  2:373714‑M2/120‑1 (MQ=255)
                                                                                                               cAGCTTCGCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCTATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATGCTCCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACg                         <  2:117205/149‑1 (MQ=255)
                                                                                                                       cGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCCCCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATccac                 <  1:178782/149‑1 (MQ=255)
                                                                                                                       cGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGGGCCAGAATCGAGAGCAGATCATCCACCGGGTAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACCGTATcccc                 >  1:4220/1‑147 (MQ=255)
                                                                                                                        gACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCCTACAGCGATGACGTTTACTTTCGAGTGCCCGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACACGCCCTGATCTGCGGTCTCGCCATACGGTATccccc                >  1:34900/1‑149 (MQ=255)
                                                                                                                           aaTCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTGTACTTTGGAGTGCGAGAATCGAGAGCAGATCATCCACCGGAGAGTTACCATACGCGCCCTGATCTCCCGTCCCGCCCTACGGTATCCACcaca             >  2:336632/1‑149 (MQ=255)
                                                                                                                              ctctACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCacacac          >  1:502823/1‑149 (MQ=255)
                                                                                                                                   ccGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCACCCTGATCTGCCGTCTCGCCCTCCGGTATCCCCCTCAAACgaaac     >  2:350640/1‑145 (MQ=255)
                                                                                                                                      gtacggtacCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          <  1:48602/93‑1 (MQ=255)
                                                                                                                                      gtacggtacCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          >  2:48602/1‑93 (MQ=255)
                                                                                                                                      gtacgctacCGAGATCTTCACCAACCACCATACAGCGATGACGTTTACTTTCGGGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATc  <  2:40850/149‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                              
TGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATC  >  NC_000913_3_pae_tpiA/3548433‑3548715

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑