Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,560,7780TC53.1% 17.0 / 39.7 32E51G (GAA→GGA) ddpBD,D‑dipeptide ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (5/10);  new base C (0/17);  total (5/27)
Fisher's exact test for biased strand distribution p-value = 1.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.58e-04

AGCGTCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATACTCCAGAAGGTC  >  NC_000913/1560628‑1560927
                                                                                                                                                      |                                                                                                                                                     
aGCGTCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATAtttt                                                                                                                                                       >  2:67818/1‑151 (MQ=255)
aGCGTCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATAtttt                                                                                                                                                       >  1:543730/1‑151 (MQ=255)
  cGTCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTcc                                                                                                                                                     <  2:436525/151‑1 (MQ=255)
    tCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCa                                                                                                                                                    <  1:737357/150‑1 (MQ=255)
      gCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGa                                                                                                                                                 <  1:187977/151‑1 (MQ=255)
           gAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCa                                                                                                                                            <  1:469093/151‑1 (MQ=255)
            aaaaaTATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCAt                                                                                                                                           <  2:80107/151‑1 (MQ=255)
                       cAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCgg                                                                                                                                <  2:746351/151‑1 (MQ=255)
                           tctTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCAc                                                                                                                            >  1:187212/1‑151 (MQ=255)
                              tCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCAccc                                                                                                                          >  2:200662/1‑150 (MQ=255)
                              tCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCAc                                                                                                                            <  2:35605/148‑1 (MQ=255)
                              tCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCAc                                                                                                                            <  1:658734/148‑1 (MQ=255)
                                   cACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGt                                                                                                                    >  1:142218/1‑151 (MQ=255)
                                       ggACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAAcc                                                                                                                >  2:135374/1‑151 (MQ=255)
                                                    gAATGTATGTCCCAGGGCCACCAGAAAACGGGTCGCTGACGGAGCGGAAAAACTTTACATACAGGGGCTGGCCCAGCCCCAGTTGCGGGCAAATTTTTCCCGGGATGGCATCGCGGGCGCGGTCACCCGCCAGTAACCGCGCCGGATc                                                                                                      <  2:88939/148‑1 (MQ=255)
                                                        ggATGTCCCCAGGTCACCATAAAACGGGTCGCTGACGTAGCGGAAAAACTGTACATACGGTGGCTGGTCCAGCCCCATTGGCTGGCAAATATTTCCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAggg                                                                                               <  1:655044/151‑1 (MQ=255)
                                                        gaaTGTTCCCAGGTCCCCATAAAACAGGTCGCTGACGTGGCGGAAAAACTTTACATACAGTGGCTGGCCCAGCCCCGGTTGCTGGCGAATTTTTCCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAg                                                                                                 <  2:187205/147‑1 (MQ=255)
                                                           tGTCCCCAGGTCACCATAAAACAGGTCGCTGACGTAGCGGTAAAACTTTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGATTATTTCCCACGATAGCATCGCTGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGa                                                                                              <  1:292672/149‑1 (MQ=255)
                                                             tccccAGGTCCCCAAGAAACGGGTCGCTGACGTAGGGATAAAACTGTACATACAGTGGCTGTTCCAGCCCCATTTGCGGGCAAATTTTTCCCACGATAGCAGCGCGGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGAt                                                                                             <  2:377316/146‑1 (MQ=255)
                                                               cccAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAACCTTTACATACAGGGGCGGGCCCAGCCCCAGTTGCGGGCAAATATTTCCCACGATAGCAGGGCTGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGa                                                                                              <  2:416221/145‑1 (MQ=255)
                                                               cccAGGACACAAGGAAACGGGTGGCTGAGGTAGGGGAAAAACTGTACATACGGGGGCTGGCCCGGTCCCGGTGGCGGGCGAATATTTCCCACTATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGAt                                                                                        <  1:690519/151‑1 (MQ=255)
                                                                     tccccATGAAACGGGTCGCTGACGTAGCGGAAAAACTTTACATACAGTGGCTGGTCCAGTCGCATTTGCTGGCGATTATTTCCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCgag                                                                                   <  1:611311/147‑1 (MQ=255)
                                                                          ataaaaCGGGTCGCTGACGTAGCGGTAAAACTGTACATACGGTGGCTGGTCCAGCCCCAGTTGCGGGCAAATATTTTCCACGATAGCATCGCGGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGataata                                                                             <  2:566110/148‑1 (MQ=255)
                                                                                  ggTCGCTGACGTAGCGGAAAAACTGTACATACAGGGGCTGGCCCAGCCCCATTTGCGGGCAAATATTTCCCACGATAGCATCGCGGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAAt                                                                     <  2:338139/151‑1 (MQ=255)
                                                                                               gCGGTAAAACGTTACACCCAGGGGTTGTTCCGGCCCCAGTGGCGGGGGAATATTTCCCACGAGAGCTCGGCGGGGGCGGGCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCa                                                               <  2:181043/144‑1 (MQ=255)
                                                                                                  gaaaagCTTTACACACGGTGGCTGGCCCGGCCCCAGTGGCGGGAGAATATTTTCCACGATAGCAGCGGGGGCGCGCTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGAcgcccg                                                       <  2:143428/147‑1 (MQ=255)
                                                                                                                            ccggccccATTTGCGGGCGAATTTTTCCCCCGATACCATCGCGGGCGGGTTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCagcagc                            <  1:501177/145‑1 (MQ=255)
                                                                                                                               gTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTg                        >  1:405432/1‑151 (MQ=255)
                                                                                                                                 cccggtggggggCAAATATTTCCCTGGATACCTTCGCTGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGc                      <  1:210270/141‑1 (MQ=255)
                                                                                                                                   cAGTTGCGGGCGATTTTTTCCCAGGATAGCAGCGGTGCCTCGCCCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTg                        <  1:245194/147‑1 (MQ=255)
                                                                                                                                          gggagAATATTACCCAGGATAGCTTCTGGGGCGAGGTCCTCCGCCAGTAACCTCGCCGGATCACCAGGGATCAGATTCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTaa                  <  1:494258/142‑1 (MQ=255)
                                                                                                                                               attatTTCCCACGATAGCATCGTTGGCGCGGTCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATa              <  1:417967/143‑1 (MQ=255)
                                                                                                                                               aaTTTTTCCCCCGATACCACCTCGGGCGCGTCCCCCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATACTCCAg        <  2:461368/151‑1 (MQ=255)
                                                                                                                                                atatTTCCCACGATAGCACCGCGGGCGCGGCCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATACTCCAGa       <  1:186840/151‑1 (MQ=255)
                                                                                                                                                     ttCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATACTCCAGAAGGTc  >  2:359133/1‑151 (MQ=255)
                                                                                                                                                      |                                                                                                                                                     
AGCGTCGCCGGGAAAAATATACGCAACTCTTCCAGCACCGGACGCCCGGTACGAATGGATGTTCCCAGGTCACCATGAAACAGGTCGCTGACGTAGCGGTAAAACTGTACATACAGTGGCTGGTCCAGTCCCAGTTGCTGGCGAATATTTTCCACGATAGCATCGCTGGCGCGGTCACCCGCCAGTAACCGCGCCGGATCACCAGGGATCAGATGCGAGATAATAAACGTAATCACGCAGACGCCCGCCACCACGAGCACCAGCCCCCAGCAGCGTTGGCGTAAAATACTCCAGAAGGTC  >  NC_000913/1560628‑1560927

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑