Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	225,467	1	.	T	41.7%	13.0 / 21.8	12	intergenic (+10/‑33)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
Reads supporting (aligned to +/- strand):  ref base . (3/4);  new base T (4/1);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 2.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.21e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGTCCACTCAGGCCTACCAAATTTGCACG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACTTCAGAGTGTACC  >  NC_000913_3_pae_pgi/225439‑225615                              |                                                                                                                                                     aGTCAACTCAGGACTACCAACTTTGCACG‑GCAAATTTGAAGAGGTTTTAACTACAAGTTATGAGGCTAAAGCTAAGCTGGGAGAGCACCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATCGCTCCACCCTACCTGTAGTGGt                             >  2:136520/1‑150 (MQ=11)      gcTCGGGCCTACCAAATGTGCACG‑GAAGATGTGAAGAGGTTTTAACTACATGTTATGGGGCTAGAGCTCAGTTGGGAGAGCGCGTGCTTTGCACGCGGGAGGTCTTCGGTTAGATCCCGCATTGCTCCACATTCTCTGTAGTGGTtaaat                        <  2:230194/149‑1 (MQ=11)          aGGCCTACCAAATTTGCACG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATaaaa                    <  2:104397/150‑1 (MQ=32)          aGGCCTACCAAATTTGCACG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATaaaa                    >  2:540006/1‑150 (MQ=32)             ctcttcAAATTTGCCGT‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAAt                 >  2:479353/6‑150 (MQ=11)                ttcAAATTTGC‑CGTGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGtt                            >  1:428610/3‑136 (MQ=255)                ttcAAATTTGC‑CGTGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGtt                            <  2:428610/134‑1 (MQ=255)                 tcAAATTTGC‑CGTGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACtt             >  1:135343/2‑150 (MQ=255)                 tcAAATTTGC‑CGTGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACtt             >  1:663928/2‑150 (MQ=255)                 tcAAATTTGC‑CGTGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACtt             >  1:99895/2‑150 (MQ=255)                        tGCACG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACTTCAGAgtg      <  1:177498/150‑1 (MQ=32)                            cG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACTTCAGAGTGTAcc  <  4:180552/150‑1 (MQ=32)                              |                                                                                                                                                     AGTCCACTCAGGCCTACCAAATTTGCACG‑GCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGGTTAAATAAAAAATACTTCAGAGTGTACC  >  NC_000913_3_pae_pgi/225439‑225615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑