Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24403,130,7180TG27.8% 50.0 / 11.2 36intergenic (+89/‑201)livF_3/oprD_7High‑affinity branched‑chain amino acidtransport ATP‑binding protein LivF/Porin D
Reads supporting (aligned to +/- strand):  ref base T (8/18);  new base G (10/0);  total (18/18)
Fisher's exact test for biased strand distribution p-value = 3.44e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCGCGGGAAGATATTCAGCATTTCTACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTTTGTTGGCATGGT  >  KT2440/3130585‑3130852
                                                                                                                                     |                                                                                                                                      
gcgcgGGAAGATATTCAGCATTTCTACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGttt                                                                                                                                      >  8:56561/1‑136 (MQ=255)
                  cATTTCTCCCGGGGCGGCAAGGGCGGACGGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGGCATACCGCCTTTTCCTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGaaa                                                                                                                     <  1:192487/135‑1 (MQ=255)
                   aTTTCTACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTTTTTTCGCCCTGACGAAAgc                                                                                                                   >  7:262900/1‑136 (MQ=255)
                      tCTACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAgcg                                                                                                                  <  2:101881/134‑1 (MQ=255)
                        tACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTAGCCCTGACGCAAgcgcag                                                                                                               >  4:38183/1‑133 (MQ=255)
                                  gcAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCGTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGGGTTTTGGGCCGGACGGAAGCCCGGTGGCGCCGGc                                                                                                     >  5:14279/1‑135 (MQ=255)
                                    aaGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCaa                                                                                                   <  3:212558/135‑1 (MQ=255)
                                            actgaGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTGGCCCGGGCGCAAGCGCGGTGGGGCCGGCCACAGCAGtt                                                                                           >  2:120396/1‑135 (MQ=255)
                                                   ggTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTTTTTTGGGCCGGGCGCAAGCGCGGTGGCGGCGGCAACCGCCGTTGTGCAGa                                                                                    >  1:168734/1‑135 (MQ=255)
                                                    gTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTGGCCCTGACGCACGCGCTGTGGCGCCGGCACCAGCCGTTGTGGAGAt                                                                                   >  6:50446/1‑135 (MQ=255)
                                                    gTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGCAAGCGCGGTGGCGCCGGGCACAGCCGTTGTGCAGAtt                                                                                  >  8:43689/1‑136 (MQ=255)
                                                     tGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCCGGCCGCGGTTTTTTTGCCCCGCGCACAGCGCTGTGGGGCCGGCAACAGCCGTTGTGGGGAtt                                                                                  >  4:39896/1‑135 (MQ=255)
                                                     tGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTGTTTTGGGGCGGGCGCAAGCCCGGTGGGGCCGGGGACCGCCGGTGTTCAGaat                                                                                  >  1:293787/1‑133 (MQ=255)
                                                       gCGACGGGTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCt                                                                               <  7:56561/136‑1 (MQ=255)
                                                       gCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGc                                                                                <  2:99291/135‑1 (MQ=255)
                                                       gCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTGCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGc                                                                                <  6:157619/135‑1 (MQ=255)
                                                          aCGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTTTTTTTGCCCGGACGCAAGCGCGGTGGCGCCGGCAACAGCCGGTGTGCAGATTgggtcg                                                                            >  8:161660/1‑131 (MQ=255)
                                                            ggCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGc                                                                           <  3:38183/135‑1 (MQ=255)
                                                            ggCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGc                                                                           <  2:8173/135‑1 (MQ=255)
                                                              cTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAg                                                                         <  1:79076/135‑1 (MQ=255)
                                                              cTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGACAACAGCAGTTGTGCAGATTGCTTCGCAg                                                                         <  6:104960/135‑1 (MQ=255)
                                                                 tgGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACg                                                                      <  7:258399/135‑1 (MQ=255)
                                                                     gcggcgCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGca                                                                 <  7:161660/136‑1 (MQ=255)
                                                                         cgcAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGcatca                                                              <  2:37955/135‑1 (MQ=255)
                                                                                    cGCTTTTTACTGCCTCGGGCAGGTCCCATCCACCGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAgg                                                   <  5:178571/135‑1 (MQ=255)
                                                                                      ccTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGCGCATCATAGTGTTGAGGaa                                                 >  6:296870/1‑135 (MQ=255)
                                                                                           tACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTTGCCCTGTCGAAAGCGCGGTGGGGCCGGCCACAGCAGTTGTGAAGATTTAATGGCCGAAGGTGCAACATAGTTTTGAGGAAgttgt                                            >  2:83730/1‑135 (MQ=255)
                                                                                           tACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGGTTTTTTCGCCCGGACGCAAGCGCTGTGGCGCCGGCCACCGCAGTTGTGCAGATTGCTTCGCAGCCGGAGCATCATAGTGTTGAGGAAgttgt                                            >  6:242480/1‑135 (MQ=255)
                                                                                                   aGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTAGCCCGGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGACGATTGCTTCGCAGACGGAGCATGATATTGTTGATGAAGTTGTTCAAtttc                                    >  6:110017/1‑133 (MQ=255)
                                                                                                    ggTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCCCCGCCAACACCACATGTGCAGATTTCTTCGCAGACGCAGCATAATACTGTTGAGGAAGTTGTTCAAATGCtt                                  >  7:172868/1‑136 (MQ=255)
                                                                                                               aTTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAACGCGCTGTGGCGGCCGCAACAGCAGTTGTGCAGATTGCTACGCAGACGGAGGAACAAAGTGTTGAGGAAGGTGTTCAATTGCTTGAAATACAATg                       >  8:52502/1‑136 (MQ=255)
                                                                                                                ttCAACGCGGCCCAGGCCGCGGGTTTTTCGGCCGGACGCACGCGCTGTGGCGCCGGCCACCGCAGGTGTGCAGATTGCTTCGCAGACGGAGCATCATATTGTTGAGGAAGTTGTTGAATTGATTGAATAAAAATg                       >  4:240241/1‑135 (MQ=255)
                                                                                                                  cAACGCGGCCCAGGCCGCGGGTTTTTAGCGCCGGCGCAAGCGCGGGGGCGCCGGCCACCCCCGGGGTGCCGATTGGGTGGCAGACCGCGCCAGAAAGTGTTGAGGCAGTTGGTCAATTGGGTGTATAACaaatgt                     >  6:254266/1‑131 (MQ=255)
                                                                                                                           ccAGGCCGCTTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTttgt           <  7:52502/136‑1 (MQ=255)
                                                                                                                             aGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTttgttg         <  8:40692/136‑1 (MQ=255)
                                                                                                                              ggcggggTTTTTTTCGCCCTGAGGAATGCGGGGTGGGGCCGGCACAAGAAGTGGGGCATTTTGCTTCGCCGACGGAGAATCATCGTGTGGAGGATGTTGTTCAATTGATTTAAAAACAATGGTTTTTTTttgttg         <  2:265436/129‑1 (MQ=255)
                                                                                                                              ggCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTttgttg         <  6:103928/135‑1 (MQ=255)
                                                                                                                                     tttttttCGCCCTGACGAAAGCGCTGTGGCGCCGGCTACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTTTGTTGGCATGgt  <  2:184001/135‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                      
GCGCGGGAAGATATTCAGCATTTCTACCTGGGCGGCAAGGGCTGACTGAGCGGTGGCGACGGCTGTGGAGCGGCGCAGTCATACCGCCTTTTACTGAGTAGGTGATGTTCCATTCAACGCGGCCCAGGCCGCGTTTTTTTCGCCCTGACGAAAGCGCTGTGGCGCCGGCAACAGCAGTTGTGCAGATTGCTTCGCAGACGGAGCATCATAGTGTTGAGGAAGTTGTTCAATTGCTTGAATAACAATGGTTTTTTTTTGTTGGCATGGT  >  KT2440/3130585‑3130852

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑