Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273645,9200AT50.0% 12.1 / 11.4 23R9R (CGT→CGA) citEcitrate (pro‑3S)‑lyase subunit beta
Reads supporting (aligned to +/- strand):  ref base A (2/9);  new base T (11/0);  total (14/9)
Fisher's exact test for biased strand distribution p-value = 2.21e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GGCGGTGTCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATT  >  NZ_CP009273/645782‑646050
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ggcggTGTCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTa                                                                                                                                      <  1:463318/139‑1 (MQ=255)
     tgtCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGGGAGGTTTTCggtt                                                                                                                                 >  1:589343/1‑136 (MQ=255)
           tttCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGGGGGGTTTATG‑TTTTTGGAg                                                                                                                          >  2:567196/1‑139 (MQ=255)
               aCGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGGTTTTCG‑TTGTTGCAGC‑g                                                                                                                       >  1:220560/1‑137 (MQ=255)
                             aGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGGGGTTTTCG‑TTGTTGCAGC‑GAAACGGAAATCATTgg                                                                                                       >  2:587433/1‑139 (MQ=255)
                               tCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGGGAGGTTTTCG‑GTTTTTCAGC‑GAAGCGGGAAACATTGGc                                                                                                      >  2:407862/1‑138 (MQ=255)
                                 ttCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGGGAGGTTTCCG‑CTGTTGCAACGGAAGGGGAAA‑CATTGGCAAt                                                                                                   >  1:385816/1‑139 (MQ=255)
                                 ttCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGCGGGGTTTTCGTTTTTTGCA‑C‑GAAGCGGGAATCATTTGGAAt                                                                                                   >  1:562934/1‑139 (MQ=255)
                                      ggTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAAtcctcc                                                                                              <  1:567196/139‑1 (MQ=255)
                                         cAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGGGGGGTTTTCG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTcccct                                                                                           >  2:263076/1‑137 (MQ=255)
                                                      aTCAGCCGGGTAGATGAAGGAGTTGCTGAGCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGa                                                                              <  2:467962/139‑1 (MQ=255)
                                                      aTCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGa                                                                              <  2:332983/139‑1 (MQ=255)
                                                      aTCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGa                                                                              <  2:408722/139‑1 (MQ=255)
                                                      aTCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGa                                                                              <  2:572302/139‑1 (MQ=255)
                                                                  gATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGgcg                                                                   <  1:587433/138‑1 (MQ=255)
                                                                   aTGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTTCG‑TTGTTGCAGC‑GAAGCGGGAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGcgcg                                                                 >  1:21015/1‑139 (MQ=255)
                                                                            ttGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGGGTTTTTCG‑TTTTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCCTGGCAGAGCCGGGGTACCGCTGGCGCGGGGcagcag                                                        >  1:219494/1‑139 (MQ=255)
                                                                                                 gCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTa                                    <  2:170023/138‑1 (MQ=255)
                                                                                                 gCACCAGGCACAAACAACATGCTGCGGCGGGGGCGGGGTTTTCG‑TTTTTGCAGC‑GACACGGAAATCATTGGGAATCCCCCCCTGGCCGAGCCGGGGGAACCCCGGCGCGGGGCCGCCCGGCCTCCCCTCGTGCACgca                                    >  2:303770/1‑136 (MQ=255)
                                                                                                       ggCACAAACAACATGCTGCGGCGGGGGCGGGGTTTACG‑TTTTTGCAGC‑GAAACGGGAATCATTGGCAATCCTCCCCTGGCAGAGGCGGGGTACCGCTGGCGCGTGCCAGCAGGGGTTTCAGTCGTGCACGGAAAATg                               >  1:170023/1‑137 (MQ=255)
                                                                                                                      ctgcGGCGGGTGCGAGGTTTTCG‑TTGTTGCAGC‑GAAACGGGAAACAATGGGAATCCTCCCCTGGCAGAGCCGGGATACCGCCGGGGCGTGCCAGACGGGCTTTCAGGAGGGCCAGGAAAATGCAGTCCCGGGGGCCttt              >  2:617463/1‑139 (MQ=255)
                                                                                                                          ggcggGTGCGGGTTTTTAG‑TTGTTGCAGC‑GAAGAGGAAATAATTGGGAATCCTCCCATGGCAGAGCCGGGATACAGCGGGCGCGTGCCAGCAGGGCTTTCAGTCGTGGACGGAAAAAGCAGTCCCGTGGGCCTTTGTCa          >  2:545374/1‑139 (MQ=255)
                                                                                                                                tGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACa    <  2:562934/139‑1 (MQ=255)
                                                                                                                                  caggTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCGCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGAAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGCCAtt  <  2:507092/136‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                    
GGCGGTGTCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGCGAGTTTTACG‑TTGTTGCAGC‑GAAGCGGAAATCATTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATT  >  NZ_CP009273/645782‑646050

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑