Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,205	0	T	C	45.5%	‑4.7 / 10.3	11	intergenic (‑227/‑479)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (2/4);  new base C (3/2);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 5.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.12e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTG  >  NC_000913/565976‑566449                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                     cATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTGTTCGATGAACTCCTGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATg                                                                                                                                                                                                                                 <  1:136664/251‑1 (MQ=255)                                      ccTGGACAGTATGAAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGc                                                                                                                                                                                             >  1:127570/1‑250 (MQ=255)                                                          gaCTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAgg                                                                                                                                                                                                                             <  1:136720/198‑1 (MQ=255)                                                                                    aagtgattgcgcctACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcac                                                                                                                                                              <  1:57196/222‑1 (MQ=255)                                                                                                   cccGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTGTTCATCCCGCTCAATCACGACATAATGCAGGCCGTCACGCTTCATACGCGTGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAgn                                                                                                                                 <  1:16758/249‑2 (MQ=255)                                                                                                                               ctccATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTAATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGctgactt                                                                                                                           >  1:155255/3‑221 (MQ=255)                                                                                                                                           ccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGTAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGa                                                                                        >  1:161886/1‑250 (MQ=255)                                                                                                                                                       ccAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCAGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCACTCACGACATAATGCAGGCCTCCACGCTTCATACGCGGGTCATAGTTGGCAACGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGACATCCCGGGAGGt                                                                           >  1:23960/1‑251 (MQ=255)                                                                                                                                                                                       gATGAACTCCGGCACCATCGCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCGTGCGCGGGTCATAGTTGGCAAAGTACCAGGCAGCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCGTGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCgn                                                                                                  <  1:29154/196‑2 (MQ=255)                                                                                                                                                                                                                  aCTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCCGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGGCTTATCCGTGGAAATCg                >  1:12406/1‑251 (MQ=255)                                                                                                                                                                                                                                 ttCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCGCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTAGGGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACtg  <  1:154970/250‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                     CATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTG  >  NC_000913/565976‑566449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑