Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24401,123,2380CA64.3% ‑6.3 / 10.0 29intergenic (‑240/+64)gcvH_1/CJ019_01062Glycine cleavage system H protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (3/7);  new base A (18/0);  total (21/8)
Fisher's exact test for biased strand distribution p-value = 1.01e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.28e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGC  >  KT2440/1123105‑1123365
                                                                                                                                      |                                                                                                                               
aaTAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCt                                                                                                                              >  7:285329/1‑137 (MQ=255)
                           ccGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGGTACGACGTAGCGAAAAAGATACATttgg                                                                                                   >  1:79440/1‑137 (MQ=255)
                            cttatttattGTGTGGACTGATATCGTTCCAGGGCCCTCTGCGCGGAAACGGGTTTCACCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTAGCGTTTG‑CGCTCCCACGTAGCGAAAACGATACATgtggt                                                                                                  <  2:500/135‑1 (MQ=255)
                                        gtgGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCTAAGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGc                                                                                      >  8:111023/1‑137 (MQ=255)
                                           gAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCGTCGACGGAGGGGAAACCAAACATGTGGGTCCTGGGCTggggcg                                                                                   >  3:338640/1‑133 (MQ=255)
                                            aaTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGGTACGACGTAGCGCAAACGATACAATTGGTGCCTGGCATGGCGAgg                                                                                  >  5:248215/1‑137 (MQ=255)
                                            aaTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGGAGTATCGAACACGATAAATGTTGTGGCTGGACGGGCGAgg                                                                                  >  2:244876/1‑137 (MQ=255)
                                            aaTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGACGTTGCGAAAACGATAAATGTGGTGCCTGGACTGGCGAgg                                                                                  >  3:162194/1‑137 (MQ=255)
                                                      ttACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATggg                                                                        >  4:316795/1‑136 (MQ=255)
                                                         cAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGGGACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCtt                                                                     >  4:138792/1‑137 (MQ=255)
                                                         cAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTAAGACGGAGCGAAAACCATACATGTTGTGGCTGGACTGGCGAGGTGGCAATGGCCtt                                                                     >  3:1362/1‑137 (MQ=255)
                                                           ggTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTTCGACGGATCGAAAACGATAAAAGTGGTGGCGGGACTGGGGAGGTGCCAATGGCCTTCg                                                                   >  3:113235/1‑137 (MQ=255)
                                                              cccTCTGAGAGCAACAGGTTTCCCCCAACAAACCCTTTGCCACCTACGGGGAGGCGGCTTTTAAGCTTTTC‑CGAACCGCCTTATCCAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTc                                                                <  8:233690/136‑1 (MQ=255)
                                                                  ctGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGACGTAGCGAAAAAGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCAtgt                                                            >  1:101650/1‑135 (MQ=255)
                                                                   tGATAGCAAATGGGTTTGACCATCAAACCGTTGTGCACCGCCGGCGAGTCGGCTGTTTATCTTTTT‑CGCTCCCACGTAGCTAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCAtctc                                                           <  4:162194/137‑1 (MQ=255)
                                                                       agaaaacGGGTTTGACAACAAAACCTTTGGGCACCGCGGGGGCGGTGGGTGTGAATCTTTTG‑CCCAACGACGAAGCAAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACtt                                                       <  4:1362/134‑1 (MQ=255)
                                                                           aatgggTTTGATCATAAAACCCTTGTGCACCGACGTCGAGGAGGTTTTTTTTCGTTTT‑CGCTACTAGTTAGCTAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTcag                                                   <  7:272920/134‑1 (MQ=255)
                                                                             aGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTTCCAATGGCCTTCGGTCATATAACTTTaagca                                                 >  8:272920/1‑137 (MQ=255)
                                                                             aGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCGACGCCGTAGAGAAAAAAATAAAAGTGGTTCCTGGGCAGGGGAGGGGCCAATTGCCTTAGGTAATATCACgttacaca                                                 >  2:307536/1‑132 (MQ=255)
                                                                               ggTTTGAGCATCAAACCCTTGTGCCCCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGCCGTTGGGAAACAGATACAGGTGGTGCCTGGACGTGCGCGGTGCCAATGGCCTTCGGTCATCTCACTTTgagctgt                                               >  6:179293/1‑134 (MQ=255)
                                                                                gTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTACGGCGTAGCGCCAAAGATTCATGTGGTTGCTGGTCTTGCGCGGTGCCAATGGCCATCGGTCAGGGGACTTTGAGCAgat                                              >  2:267240/1‑137 (MQ=255)
                                                                                            accccTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑ATCTTAGACGTAGCGTAAACGCTACAGGTGGTGCCCGGACTGGCGAGGTGCCAATTGGCATCGGTCATCTCAATTTAACCAGATGATCCCGCGaaa                                  >  8:212467/3‑137 (MQ=255)
                                                                                                     gCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCGAAGACGGAGCGCAAACCAAAAATGTGGTGGCGGGACGGGGGATGTGCCCATTGGCGTGGGGGAGATCACATTAAGCAGATTATACAGCGCAAACCCGCCgg                         >  6:226455/1‑137 (MQ=255)
                                                                                                            cGGCGAGGAGGCTGTGTATCGTTTT‑AGCTAAAACCTAGCGAAAAAGATAAAAGTGGTTCCTGGTATGGCGAGGTGACAAATGCCAGACGTCAGATCACTTTCATGAACTGATGCACCGAAAACGCGCCCGCCCcgcg                  >  8:116244/1‑137 (MQ=255)
                                                                                                              gCGAGGAGGCTGTGTATCGTTTT‑CGCTACGCCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCggg                >  8:88918/1‑137 (MQ=255)
                                                                                                               cGAGGTGGCTGTGT‑TGGTTTTCCGCTCCGAGGAAGCCAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCGCGGGc               <  7:117489/137‑1 (MQ=255)
                                                                                                                      gCTTTGTATCGTTTT‑GGCAACGACGTAGCTAAAAATATACTTGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAgg        <  6:248215/137‑1 (MQ=255)
                                                                                                                          tgtATCTTTTG‑CGCTCGTACTTTGCTAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGGCAATGGCCGTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGagca    <  7:104358/137‑1 (MQ=255)
                                                                                                                            tATCGTTTT‑CGGTACGGCCTGGGGGAAAAGATACATGTGGGGGCGGGCCTGGCGCGGTGCCCATGGCCGTCGGGCATCGGACTTTTAGCGGCTGCTCCCACGGAAACGCGCCGGCGCCTCGGGCCGCCAGGggcaga  >  6:290407/1‑136 (MQ=255)
                                                                                                                                      |                                                                                                                               
AATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGC  >  KT2440/1123105‑1123365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑