Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,565	0	A	G	35.7%	0.1 / 10.5	14	intergenic (‑587/‑119)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base A (5/4);  new base G (3/2);  total (8/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.33e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGG  >  NC_000913/566321‑566763                                                                                                                                                                                                                                                      |                                                                                                                                                                                                       gCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGGACGAGTATTGCCGGAAGCGTGGCTTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGTGTGGTTACCAACTTGTACCAGAACAGGCTTGCCAATTCGCTGGCTGACGCGCAATGACGGCGCAAGGCTGCCGATGAACT‑GGCCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATan                                                                                                                                                                                                  <  1:17574/251‑2 (MQ=255)                                                                                                                    aaCGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACAGGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACGTCCTGTCATGGGCGGGAGACCTCTAAAGCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATg                                                                               <  1:112672/251‑1 (MQ=255)                                                                                                                          cactACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTCAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGc                                                                         >  1:92595/4‑251 (MQ=255)                                                                                                                                          ncAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTc                                                         >  1:30141/2‑251 (MQ=255)                                                                                                                                                         ncATGCGGGCCAATGCGCTGGCTGACGAGGAATTACGCCACCAGGCTGCAGATGAACT‑GACCTGTCTCCCAGCGCAAATTAACCGCGGTGAGAAGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCACTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGc                                          >  1:15663/2‑251 (MQ=255)                                                                                                                                                                                                   aaggccgcagatgagcttgtccatATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAGCAACGTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGGGCTGGCGAAGAGCGCAGAAATCAAATCTAAGGACGGACTGAAAGGAGCAAGTTGATGGCGCGCAAAGATGCTATTATTCATTACCTGGGGACACATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAgg  <  1:165391/227‑1 (MQ=255)                                                                                                                                                                                                        gCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAAc                                                                                                                                                                                            >  1:169882/1‑58 (MQ=255)                                                                                                                                                                                                        gCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTg                                                                                                                                               <  1:137506/103‑1 (MQ=255)                                                                                                                                                                                                          cGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAg                                                                                                                                                             >  1:1853/1‑87 (MQ=255)                                                                                                                                                                                                          cGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAg                                                                                                                                                             <  2:1853/87‑1 (MQ=255)                                                                                                                                                                                                                    gACCTGTATCAAAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTACACCTCTAAATAGTGCACACGCTCTGGCGACGATCGCAGAAATTAAAGCTCAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCa                                                                >  1:139856/1‑171 (MQ=255)                                                                                                                                                                                                                        catATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACCACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATaata                                    >  1:85248/3‑193 (MQ=255)                                                                                                                                                                                                                                      aaTTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAg                      <  1:149551/195‑1 (MQ=255)                                                                                                                                                                                                                                           aCCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACggg                                                                          >  1:4504/1‑138 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                       GCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGG  >  NC_000913/566321‑566763

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑