Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,173	0	C	G	45.5%	‑2.1 / 14.6	11	intergenic (‑195/‑511)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base C (2/4);  new base G (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 = 8.04e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CGAATACGAGGCATACCATATTTCATTTCTGCGGAAGAGTGACATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGT  >  NC_000913/565934‑566376                                                                                                                                                                                                                                                |                                                                                                                                                                                                            cGAATACGAGGCATACCATATTTCATTTCTGCGGAAGAGTGACATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCaa                                                                                                                                                                                                   >  1:3973/1‑250 (MQ=255)                    attgcatttcTGCGGAAGAGTGACATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTc                                                                                                                                                                                <  1:41985/246‑1 (MQ=255)                                           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)                                                                                                                                                                                                                                                |                                                                                                                                                                                                            CGAATACGAGGCATACCATATTTCATTTCTGCGGAAGAGTGACATTTTCTTTCCTCTGTTATGCCATCACCCGCGCTCACCTGGACAGTATGCAGCGGAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGT  >  NC_000913/565934‑566376

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: ‑