Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,392,517	G→A	noncoding (46/76 nt)	glyX →	tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,392,517	0	G	A	93.8%	36.4 / ‑6.3	16	noncoding (46/76 nt)	glyX	tRNA‑Gly
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (9/6);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

GCAGAGGGAAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTT  >  NC_000913/4392277‑4392712                                                                                                                                                                                                                                                 |                                                                                                                                                                                                    gCAGAGGGAAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGtt                                                                                                                                                                                            <  1:29272/250‑1 (MQ=255) gCAGAGGGAAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTc                                                                                                                                                                                           <  1:21477/251‑1 (MQ=255)                   cGTATAATGCGCCTCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTc                                                                                                                                                                         >  1:397971/1‑251 (MQ=255)                                tCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAACACAGTAGCAAAGCACAGACCACCCAAGCGGGAATTGCTCAGTTGGTAGAGCACGACCTTACTAATGTAGGTATCGCTAGTCAGAGTCTCGTTTCCCACTCCTAAAtttataa                                                                                                                                                             >  2:242843/1‑246 (MQ=18)                                      aaCGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTAAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                                                                                                      >  1:282251/1‑251 (MQ=255)                                          acgCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTAGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                                                                                                  >  1:50978/1‑251 (MQ=255)                                          acgCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCACAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGATCAGATGGTAGAGCAAGACATTGACAAGGCCGGGATCGCGAGTTCGAGATTCGTTACCCACTCCAAAATTTGAAAGTGAGGTAAgg                                                                                                                                                  >  2:341967/1‑251 (MQ=18)                                                                                                          agCACGACCTTGCCAAGGTCGGGGCCGCGCGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGCACAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCTTGAATTGCTCAGTTGTTAGAGCACGGCCATGCCAAGGTCAGGGtagg                                                                                  >  2:445847/1‑248 (MQ=17)                                                                                                            cACGACCTTGCCAAGGTCGGGGTCTCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAATAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGAGCGCGAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTAAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa                                                                                <  1:443434/251‑1 (MQ=255)                                                                                                                       cAAGGTCGGGGTCGCGAGTTCGGGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAGTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGtctc                                                                     <  1:341967/251‑1 (MQ=255)                                                                                                                        caGGTCGGGGTCTCTAGTTCTAGTCTCGTTCTCCTCTCCAAAATTTTAAAAGTTCTGCTAAGCACAGCCCACCCAAGCGGGAATAGCTCATTTGTTAGATCACGTCATTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAATTGCTGTAAGGCACAGACCACCCAAGCCGGAATAGCTCAGTTGGTAGAGCACGACCTTGTCAAGGTCGGGGTCGCGAGTTCGAGtcacg                                                                    <  1:245400/250‑4 (MQ=17)                                                                                                                                                cacgtaacccGCTCCAAAATTTGAAAAGTCCTGCAAATCACAGACTCCCCAAGCGGGAATAGCCCAGTTGGTGGAGCACGACCTCGCCAAGGCCGGGGTCTAGAGTTCGAGTCCCGTTTCCCGGCCGAAAATTGAAAAGTGCTGAAAGGCAAAGACCACGCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTtctc                                              <  2:397971/242‑1 (MQ=14)                                                                                                                                                      tCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATaa                                       >  1:96558/1‑250 (MQ=255)                                                                                                                                                                                  aaaGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGCCGCGATGCGTTATTg          >  1:291374/1‑251 (MQ=255)                                                                                                                                                                                         aGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTAGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGACGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGttt   >  1:168087/1‑251 (MQ=255)                                                                                                                                                                                          gACCTCCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGATCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGtttt  <  1:420699/251‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                    GCAGAGGGAAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAGAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTT  >  NC_000913/4392277‑4392712

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑