Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	693,779	0	T	.	73.3%	21.2 / 11.4	15	coding (24/921 nt)	unknown	Glycosyl transferase, family 2
Reads supporting (aligned to +/- strand):  ref base T (3/1);  new base . (6/5);  total (9/6)
Fisher's exact test for biased strand distribution p-value = 6.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTCTGCATCAATATCTGCAAACATTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTGTAATTATTTCTAATGGGCGTCCTAAATTTTGGAAATTTATCTCTTCATAACGAATTAGAGGTTTTATAAAAATAGTATTAACGCCTTTCTCTAACTCTTCTTGTGAAT  >  1/693556‑693968                                                                                                                                                                                                                                |                                                                                                                                                                                              tGTCTGCATCAATATCTGCAAACATTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGATtcattcataatt                                                                                                                                                                    >  1:294694/1‑247 (MQ=255)      gCATCAATATCTGCAAACATTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAattgat                                                                                                                                                                                            >  1:515784/1‑222 (MQ=255)       cATCAATATCTGCAAACATTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGattcattc                                                                                                                                                                          >  1:472238/1‑239 (MQ=255)                        aTTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATAtt                                                                                                                                         <  1:473543/251‑1 (MQ=255)                         ttCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAattgattgattgattgat                                                                                                                                                                                >  1:324060/1‑215 (MQ=255)                              cGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTatat                                                                                                                                    <  1:666454/250‑1 (MQ=255)                              cGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTatat                                                                                                                                    <  1:154853/250‑1 (MQ=255)                                                                 gCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTGTAATTATTTCTAAt                                                                                                >  1:182360/1‑251 (MQ=255)                                                                             atCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGATtcattcataat                                                                                                                                                                     >  1:416170/1‑171 (MQ=255)                                                                                              tttCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTatat                                                                                                                                    >  1:190195/1‑186 (MQ=255)                                                                                                                        ttatCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTGTAATTATTTCTAATGGGCGTCCTAAATTTTGGAAATTTATCTCTTCATAACGAATTAGAGGTTTTATaa                                         <  1:859374/251‑1 (MQ=255)                                                                                                                                      gATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGATtcattcataat                                                                                                                                                                     <  1:889811/117‑4 (MQ=255)                                                                                                                                                               cTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTGTAATTATTTCTAATGGGCGTCCTAAATTTTGGAAATTTATCTCTTCATAACGAATTAGAGGTTTTATAAAAATAGTATTAACGCCTTTCTCTAACTCTTCTTGTGAAt  >  1:499549/1‑251 (MQ=255)                                                                                                                                                                      agagaACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTatat                                                                                                                                    >  1:248383/1‑114 (MQ=255)                                                                                                                                                                              gTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATg                                                                                                                        <  1:690948/118‑1 (MQ=255)                                                                                                                                                                                         aCTATGTTCTTCATTATAACAAGGAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGttt                                                                                                                     >  1:365006/1‑110 (MQ=255)                                                                                                                                                                                                               ggAATTAATATTGCA‑‑‑‑ATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTg                                                                                                              >  1:395114/1‑95 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                              TGTCTGCATCAATATCTGCAAACATTCTGCGAACGACGGCACCTTTTCCTTGTTTAGGTTCATTGCGTACAATACAATCTAGTTTACTTGCAATTTCAAAAGTTTTATCTGTCGAATTATTATCATAAACGTAGATTTTTGCCAAAGGCAAAGCGGATCTAAATGAGAGAACAGTATCGGATATACTATGTTCTTCATTATAACAAGGAATTAATATTGCAATTGATTGATTGATTGATTGATTCATTCATAATTTACTTAATTAAAAAATCCATATTTATATTCTGTGATCATGTTTCCATCTGTAATTATTTCTAATGGGCGTCCTAAATTTTGGAAATTTATCTCTTCATAACGAATTAGAGGTTTTATAAAAATAGTATTAACGCCTTTCTCTAACTCTTCTTGTGAAT  >  1/693556‑693968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑