Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,633,996	0	G	A	63.2%	‑5.7 / 15.1	19	pseudogene (396/528 nt)	nohQ	pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin
Reads supporting (aligned to +/- strand):  ref base G (0/7);  new base A (9/3);  total (9/10)
Fisher's exact test for biased strand distribution p-value = 3.10e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCA  >  NC_000913/1633916‑1634089                                                                                 |                                                                                              attgCTTTGATTATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGc                                                                           <  2:6690353/98‑1 (MQ=0)         tattatatCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCAc                                                                   <  1:8494260/97‑1 (MQ=1)           tgctatCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCt                                                                 <  2:5477537/98‑1 (MQ=1)                tcacGTTTCATGAAATCAACATGTCGGTATTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGAt                                                            <  2:3584923/98‑1 (MQ=0)                     cttgaGGAAATCAATATGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCcgcg                                                       >  1:12761905/5‑101 (MQ=0)                     cttgaGGAAATCAATATGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCcgcg                                                       >  1:2986271/5‑101 (MQ=0)                     cttgaGGAAATCAATATGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCcgcg                                                       >  1:4952798/5‑101 (MQ=0)                     cttgaGGAAATCAATATGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCcgcg                                                       >  1:5658642/5‑101 (MQ=0)                     cttgaGGAAATCAATATGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGCCAATCcgcg                                                       >  1:12842701/5‑101 (MQ=0)                      ttaaGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACACAGCTGCACCCACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGa                                                      <  2:4507280/98‑1 (MQ=1)                                 aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGaacg                                           >  1:12358707/4‑99 (MQ=0)                                 aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTATTCGGCCATCCGCGACAGCACGAAAg                                           >  1:13918625/4‑101 (MQ=0)                                 aataTGTCGGTTTGCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGaacg                                           <  1:5003389/98‑3 (MQ=0)                                       tctgTTTTCCAGTTCCGTAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGa                                     <  2:6894158/98‑1 (MQ=0)                                        cgattttCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGaa                                    <  1:6045292/98‑1 (MQ=1)                                                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                           >  1:13605162/4‑101 (MQ=0)                                                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                           <  1:11380328/98‑1 (MQ=0)                                                  gtgccGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTcc                          <  2:5370333/98‑1 (MQ=1)                                                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCgg             >  1:928374/4‑97 (MQ=0)                                                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCgg             <  2:928374/94‑1 (MQ=0)                                                                          ccacggggTTCCCGTCGAGAATTCTGGCAATTTCCCCTGCGATCCGCGACAGCACGAAAGTCCAGAATGCGGTTTCCCCCACTTCAGCGGAGTCTCTGGCa  <  1:126558/97‑1 (MQ=1)                                                                                 |                                                                                              ATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCA  >  NC_000913/1633916‑1634089

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑