Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,651	0	T	C	47.1%	‑6.4 / 20.2	17	intergenic (‑673/‑33)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (5/4);  new base C (4/4);  total (9/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAG  >  NC_000913/566412‑566883                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                         gCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGtt                                                                                                                                                                                                                               >  1:7645/1‑251 (MQ=255)                  gAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGan                                                                                                                                                                                                                          <  1:145354/239‑2 (MQ=255)                                         tggttACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCa                                                                                                                                                                                        >  1:9360/1‑250 (MQ=255)                                                                               ctggctgACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGc                                                                                                                                                  >  1:177398/1‑250 (MQ=255)                                                                               ctggctgACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAc                                                                                                                                                                                                     >  1:74255/1‑199 (MQ=255)                                                                                                                           ccTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACCACTTCCTGTTATGGGCGGTAGACATCTACATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCACGTGTAt                                                                                                                                                                                                        >  1:175100/1‑153 (MQ=255)                                                                                                                           ccTGTAGNANAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTNCCTGTTATGGNCGGNNGACCNCNANATCGTGCACAGGCTCTGGCGAAGATCGCANAAATTAAAGCTAAGTTCGGACGGNNAGNNNCANNTGTAt                                                                                                                                                                                                        <  2:175100/153‑1 (MQ=255)                                                                                                                                       cgagAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCcgcg                                                                                                                                  >  1:50887/4‑211 (MQ=255)                                                                                                                                                 ncGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTggg                                                                                                                                                                       >  1:57847/2‑164 (MQ=255)                                                                                                                                                       tgAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAgg                                                                                                                                             <  1:71987/184‑1 (MQ=255)                                                                                                                                                         nggngATNCNNGNNCCANTAAAACAACTTCCTGTCATGGNNGGTAGACCTNTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGANTGAAAGGAGNNAGNGTATGNCNNNCNNNGANGCAATTATTCATTACCTGGNGANNCATAATNGCTTCTGTGCGCCGGACGTTGCcgcg                                                                                                                                  <  2:50887/189‑1 (MQ=255)                                                                                                                                                                 ccTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTGCTGTGCGCCGGACGTTGCCGCGCTAACAGGCGCAACAGTaaccagcataaatcagg                                                                                                <  1:126777/219‑16 (MQ=255)                                                                                                                                                                                              gggCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGGAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTAc                                                                                                    >  1:206114/1‑186 (MQ=255)                                                                                                                                                                                                gCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAggn                                                                                                                         <  1:142943/163‑2 (MQ=255)                                                                                                                                                                                                gCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCNGTGNNNNNGann                                                                                                                                          >  2:142943/1‑144 (MQ=255)                                                                                                                                                                                                         ctctAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCTTAATCTGATCTTAccc                                                                                                  <  1:29651/177‑1 (MQ=255)                                                                                                                                                                                                                               ggCGAAGATCGCAGAAATTAAAGCTAAGTGCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACAGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACGAGTAAAAAACCCCGGAAACAg  <  1:185481/251‑1 (MQ=255)                                                                                                                                                                                                                                          cAGAAANNAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATTACGGGCAAAGAGGCAATTATTCATTACCTGGGTACGCATAATAGCTTCTGTGc                                                                                                                                                  <  2:11173/96‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                         GCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAG  >  NC_000913/566412‑566883

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: ‑