Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,024,190	0	G	T	60.0%	‑1.2 / 12.0	10	intergenic (‑13/+45)	hspQ/rlmI	heat shock protein HspQ/23S rRNA (cytosine(1962)‑C(5))‑methyltransferase RlmI
Reads supporting (aligned to +/- strand):  ref base G (2/2);  new base T (3/3);  total (5/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.57e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TAACCTAACAGGGAATGGCGGACCTGCTGGCCGATACCGAATTTGCTGGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAC  >  NZ_CP009273/1024122‑1024256                                                                     |                                                                   tAACCTAACAGGGAATGGCGGACCTGCTGGCCGATACCGAATTTGCTGGCAATCATAGTCACATCCCGGGAAATCTTTACCTTTGAtata                                               <  2:295995/90‑1 (MQ=255)                                       gAATTTGCTTGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACa         >  1:225337/1‑90 (MQ=255)                                       gAATTTGCTGGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGAtata                                               <  1:281412/52‑1 (MQ=255)                                       gAATTTGCTGGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGAtata                                               >  2:281412/1‑52 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  >  1:419159/1‑73 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  >  1:457451/1‑73 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  >  1:94110/1‑73 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  <  2:419159/73‑1 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  <  2:457451/73‑1 (MQ=255)                                                               cTCCCGTGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAc  <  2:94110/73‑1 (MQ=255)                                                                     |                                                                   TAACCTAACAGGGAATGGCGGACCTGCTGGCCGATACCGAATTTGCTGGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAAC  >  NZ_CP009273/1024122‑1024256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑