Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,596,1050CA34.4% 44.0 / 28.5 32R100L (CGT→CTT) livHbranched chain amino acid/phenylalanine ABC transporter membrane subunit LivH
Reads supporting (aligned to +/- strand):  ref base C (10/11);  new base A (4/7);  total (14/18)
Fisher's exact test for biased strand distribution p-value = 7.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.97e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTTCGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAGC  >  NC_000913/3596025‑3596184
                                                                                |                                                                               
cTTCGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAc                                                                                 <  2:691993/81‑1 (MQ=255)
  tCGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACg                                                                                >  1:692053/1‑80 (MQ=255)
   cGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACg                                                                                <  1:691995/79‑1 (MQ=255)
   cGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGc                                                                               <  1:691994/80‑1 (MQ=255)
          gCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCg                                                                       >  1:692049/1‑81 (MQ=255)
              aCGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTaa                                                                   <  2:691997/81‑1 (MQ=255)
              aCGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTa                                                                    <  1:691996/80‑1 (MQ=255)
                      ttGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCAccc                                                            <  2:691998/80‑1 (MQ=255)
                         cAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGtt                                                         <  2:691999/80‑1 (MQ=255)
                            gAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGAt                                                     <  2:692000/81‑1 (MQ=255)
                               gATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACt                                                  <  1:692001/81‑1 (MQ=255)
                               gATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACt                                                  >  1:692061/1‑81 (MQ=255)
                                aTGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTc                                                 >  2:692056/1‑81 (MQ=255)
                                   gACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAg                                              >  1:692047/1‑81 (MQ=255)
                                   gACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAg                                              <  1:692002/81‑1 (MQ=255)
                                      aTACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCg                                           >  2:692050/1‑81 (MQ=255)
                                       tACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGt                                          <  2:692003/81‑1 (MQ=255)
                                       tACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGt                                          <  2:692004/81‑1 (MQ=255)
                                           gATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGgc                                      <  2:692005/81‑1 (MQ=255)
                                               gCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTg                                  >  1:692051/1‑81 (MQ=255)
                                                cAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTgg                                 >  2:692062/1‑81 (MQ=255)
                                                        aGTGCAATCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGAc                          <  1:692006/80‑1 (MQ=255)
                                                            cAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGAtt                      <  2:692007/80‑1 (MQ=255)
                                                            cAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTg                     >  2:692054/1‑81 (MQ=255)
                                                             aaTCAGGCGCTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTgc                    <  1:692008/81‑1 (MQ=255)
                                                                 aGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGcc                 <  1:692009/80‑1 (MQ=255)
                                                                   gcgcTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCcgac              >  1:692057/1‑81 (MQ=255)
                                                                    cgcTTAGAGTTAAGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCcgac              >  2:692058/1‑80 (MQ=255)
                                                                            gTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGc     >  1:692066/1‑81 (MQ=255)
                                                                              tACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAg   >  1:692065/1‑81 (MQ=255)
                                                                               aCGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAg   <  2:692011/80‑1 (MQ=255)
                                                                               aCGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAg   <  1:692010/80‑1 (MQ=255)
                                                                               aCGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAGc  >  2:692070/1‑81 (MQ=255)
                                                                                cGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAGc  <  1:692012/80‑1 (MQ=255)
                                                                                cGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAGc  >  2:692059/1‑80 (MQ=255)
                                                                                |                                                                               
CTTCGGTCAGGCTGACGTAGTTTTGCAGGAAGATGGACATACCGATTGCAGAGATGAGTGCAATCAGGCGCTTAGAGTTACGCACCGGGCGGTAAGCCACCCGTTCGATACTCCAGCCGTAGGCGCTGGCAATGACGATTGCGCCGACGAATCCCGCAGC  >  NC_000913/3596025‑3596184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑