Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	5,384,276	0	C	G	30.2%	104.6 / 12.3	53	intergenic (+539/‑319)	CJ019_05064/CJ019_05067	putative protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (3/34);  new base G (16/0);  total (19/34)
Fisher's exact test for biased strand distribution p-value = 6.53e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTGGGTCGTT  >  KT2440/5384165‑5384407                                                                                                                 |                                                                                                                                      acacGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTTTTGGTGG‑GATTTTGGGGGTGCggggggg                                                                                                             >  5:121445/1‑133 (MQ=255) acacGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGGTTTTTTTGGATGG‑AATTTTGGGGCGGAggggggg                                                                                                             >  3:331452/1‑133 (MQ=255) acacGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGGCTGG‑AATTTGGGGGCTGCGGGtggg                                                                                                             >  6:314857/1‑134 (MQ=255) acacGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CGTTTTTTTTGGCGGG‑AATTTTGGGGGGGCGGGtggg                                                                                                             >  5:306737/1‑134 (MQ=255)   acGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTTGCGGGG‑ATTTTGGG‑GGTGCGGGGCGaaa                                                                                                           >  4:162303/1‑137 (MQ=255)     ggCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGaaaaa                                                                                                         <  2:24527/137‑1 (MQ=255)       cTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATc                                                                                                       <  4:286639/137‑1 (MQ=255)          aGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCGCGGGCGT‑CGGTTTTTGTGGGTGG‑AATTTGTGGGCGGGGGGGGGAAAAATAGGa                                                                                                    >  8:290527/1‑137 (MQ=255)            cATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGAtt                                                                                                  <  4:48010/137‑1 (MQ=255)             aTGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTTTTGCTGGTAATATGGG‑GGTGCGGGGGGATAATACGGAttt                                                                                                 >  7:445984/1‑137 (MQ=255)               ttagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                               <  3:368960/136‑1 (MQ=255)               ttagtaCCGACAGCGGAGTACGGGCGTACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                               <  4:283843/136‑1 (MQ=255)               gtagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                               <  7:290527/137‑1 (MQ=255)               gtagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                               <  1:273632/137‑1 (MQ=255)               gtagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                               <  1:398892/137‑1 (MQ=255)                 agtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAAcc                                                                                             <  7:155117/137‑1 (MQ=255)                 agtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAACAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAAcc                                                                                             <  1:258935/137‑1 (MQ=255)                  gtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTTTGGCTGG‑AATTTTGGCGGGGGGGGTGGAAAAATCGGTTTTAAacc                                                                                            >  6:372172/1‑137 (MQ=255)                         cAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAAACGGATTTAACCCCGTTCtt                                                                                     >  8:461682/1‑137 (MQ=255)                         cAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCtt                                                                                     <  4:46362/137‑1 (MQ=255)                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTGTTGCGGG‑GATTTTGGCGCGGCGGGGGGGAAAAAAGGTTTTTAACCCTTtgttgt                                                                                   >  7:188591/1‑137 (MQ=255)                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTGTGGCTGG‑TATTTGGGGGCGGCGGGGCGAAAAATAGGTTTTTACCCCGTTCTTGt                                                                                   >  8:195180/1‑137 (MQ=255)                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGGTTTTTGTGGGTGG‑CATTTTGGGGGGGGGGGGGGGAAAATAGGATTTTACCCCgttagtgt                                                                                   >  3:134127/1‑132 (MQ=255)                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGG‑GTTTTTTTTTGGCGGG‑GATTTTGGGGCTGCGGGAGGCAAAATACGTTTTTACACCCTTTTTGt                                                                                   >  8:52642/1‑137 (MQ=255)                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCAACAAATACAAAGAATAAGACGCCCTCGGGCGT‑GTTTTTTTGTGGCTGG‑GAATTAGGGGCGGCGGGGCCACAAAACGGAATTTAGCCCattatttt                                                                                   >  6:397265/1‑135 (MQ=255)                              gAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑gg                                                                               <  8:168547/137‑1 (MQ=255)                               aGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑ggg                                                                              <  7:195180/137‑1 (MQ=255)                                 tACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCg                                                                            <  2:284501/137‑1 (MQ=255)                                 tACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCg                                                                            <  3:399887/137‑1 (MQ=255)                                     ggCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTc                                                                        <  3:336603/137‑1 (MQ=255)                                     ggCGGACGGGGGTTCAAATCCCCCCGGCTCCACAAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTc                                                                        <  3:337649/137‑1 (MQ=255)                                       cGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGG‑GGGTTTTTTTGGCGGG‑AAATTTGGGGCTGCGGGTGGCAAAAAAGGGTTTTACACCATTATTTTT‑GGGCGtttgcg                                                                      >  8:303709/1‑134 (MQ=255)                                         gACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CGTTTTTTGTGGCGGG‑CATTTGGGCGGTGCGGGTGGATAAATCGGTTTTAACCCCGTTCTTGTA‑GGGGGTTTACCaa                                                                    >  6:316277/1‑137 (MQ=255)                                           cGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAg                                                                  <  2:330739/137‑1 (MQ=255)                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑GGTTTTTTTTGGGGGG‑GATTTTTGGGGGGCGGGGCGCTAAATACTCTTTAACCCCGTTCGTGTATGGGGGTTTCCaaaaaaa                                                                >  4:318625/1‑134 (MQ=255)                                                     aaTCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATActgcctg                                                        <  6:212232/137‑1 (MQ=255)                                                            ccGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTTTTCCGGG‑AATTTGGGCGCTGGGGGGCGCAAAATCGGAGTTAACACCATTCGTGTA‑GGGGGTTTCCCAAAGATAATGCCTGCGccggg                                                 >  2:117267/1‑134 (MQ=255)                                                                             aaaGAAGAAGACGCCCTCGGGCGT‑GTTTTTTTGTGGCTGG‑TATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGGTTTACGTTGGGGTCAtt                                >  2:25843/1‑137 (MQ=255)                                                                              aagaagaagACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttt                               <  6:306737/137‑1 (MQ=255)                                                                                tatgaagaCGGCCTGGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGTGGCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                             <  2:447434/134‑1 (MQ=255)                                                                                gaagaagaCGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                             <  6:121445/137‑1 (MQ=255)                                                                                gaagaagaCGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                             <  7:417777/137‑1 (MQ=255)                                                                                gaagaagaCGCACTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCTGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                             <  1:153343/137‑1 (MQ=255)                                                                                caagaagaCGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGTGCCTGTTTTCCGTTGCGGTCAttttt                             <  7:193668/136‑1 (MQ=255)                                                                                     cgaCGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCTCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAgg                        <  1:397143/136‑1 (MQ=255)                                                                                       aCGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGt                      <  2:280149/137‑1 (MQ=255)                                                                                       aCGCCCTCGGGCGT‑ATTTTTTTGTGCCTGG‑AATTTGTGCTCTGCGGGTCGAAAAATCTGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCACAGTTACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGt                      <  8:348713/137‑1 (MQ=255)                                                                                            cTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAg                 <  7:111225/137‑1 (MQ=255)                                                                                              cGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGtc               <  8:268443/137‑1 (MQ=255)                                                                                               gggCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGtct              <  6:224116/137‑1 (MQ=255)                                                                                                    t‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTg         <  1:154474/137‑1 (MQ=255)                                                                                                        ttttttGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTGGGt      <  8:145077/137‑1 (MQ=255)                                                                                                            ttGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTGGGTCGtt  <  5:27332/137‑1 (MQ=255)                                                                                                                 |                                                                                                                                      ACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGT‑CTTTTTTTGTGCCTGG‑AATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTA‑GGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTGGGTCGTT  >  KT2440/5384165‑5384407

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: ‑