Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,096,5790TC58.8% 5.4 / 13.3 17intergenic (+527/+209)ycdU/serXhypothetical protein/tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base T (1/6);  new base C (5/5);  total (6/11)
Fisher's exact test for biased strand distribution p-value = 3.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTC  >  NC_000913/1096536‑1096635
                                           |                                                         
ttCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGa          <  1:468431/93‑1 (MQ=0)
 tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         <  2:1582845/93‑1 (MQ=9)
 tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         >  1:2571811/1‑93 (MQ=255)
 tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         <  2:2481462/93‑1 (MQ=255)
 tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         <  1:6076293/93‑1 (MQ=255)
  ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt        <  2:1449500/93‑1 (MQ=12)
   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc       >  1:5639682/1‑93 (MQ=255)
   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc       <  1:6058921/93‑1 (MQ=255)
   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc       >  1:844644/1‑93 (MQ=255)
    cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg      <  1:1659701/93‑1 (MQ=16)
    cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcc      >  1:6714203/1‑92 (MQ=255)
    cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg      >  1:1224927/1‑93 (MQ=255)
      tCCCCGCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgct    <  1:71090/93‑1 (MQ=255)
      cccccccGTGGTGTTCAATTTACGAAAAAAAAGCCCGTTCTTTCGTGCGAGCTCTTGTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgct    <  2:5307562/92‑1 (MQ=11)
       ccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgctt   <  1:4291500/93‑1 (MQ=255)
        cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc  <  2:3662432/93‑1 (MQ=12)
        cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc  <  2:5441348/93‑1 (MQ=12)
        cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc  >  2:4825722/1‑93 (MQ=255)
                                           |                                                         
TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTC  >  NC_000913/1096536‑1096635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑