Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,695,560	0	T	C	66.7%	4.5 / 11.0	15	I116T (ATC→ACC)	malY	bifunctional maltose regulon transcriptional repressor/cystathionine beta‑lyase MalY
Reads supporting (aligned to +/- strand):  ref base T (5/0);  new base C (0/10);  total (5/10)
Fisher's exact test for biased strand distribution p-value = 3.33e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.27e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTT  >  NZ_CP009273/1695491‑1695627                                                                      |                                                                    gCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACg                                                 >  2:402689/1‑90 (MQ=255)    cTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCAt                                              >  1:229231/1‑90 (MQ=255)          tcgtCTATATGTTTTAAAAACAGATTAGTCGGTGGTCGGAAACAGGAAACGGGGTGGTGACCCCCCCCCCCGCCTATGACGCATTTTACa                                        <  2:348984/87‑1 (MQ=255)          tCATTTATATGTTTTCAGAACTGATTCGTCAGTGGTCTAAAACGGGTGAAGGCGTGGTGACCCACACCCCCGCCTATGACGCATTTTACa                                        <  2:457245/90‑1 (MQ=255)           cATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACaa                                       >  1:114596/1‑90 (MQ=255)                       ttCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAgg                           >  1:482207/1‑90 (MQ=255)                        tCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGt                          >  1:228320/1‑90 (MQ=255)                                   tcgtcgGTGGTCTGAAACGGGTGAGGGCGTGGTGACCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGcac               <  1:402689/90‑1 (MQ=255)                                   tCGTTAGTGGTCTAAAAAAGGTGAGGGGGGGGTGACCCCCACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGcac               <  2:436042/90‑1 (MQ=255)                                   tCGTCAGTGGTCTAAAACAGGTGAAGGCGTGGTGACCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGcac               <  2:23603/90‑1 (MQ=255)                                             tcgaaaaCAGGTAAGGGGGTGGTGACCCCCACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGccc     <  2:294005/86‑1 (MQ=255)                                             tCTAAAACAGGTGAGGGCGTGGTGACCCCCCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGccc     <  1:294809/90‑1 (MQ=255)                                               taaaaCGGGTGAAGGCGGGGTGACCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGt   <  2:88215/88‑1 (MQ=255)                                                gAAACGGGTGAAGGCGTGGTGACCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGtt  <  2:228320/90‑1 (MQ=255)                                                aaaaCGGGTGAGGGGGGGGTGACCCCCACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGtt  <  1:51448/89‑1 (MQ=255)                                                                      |                                                                    GCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAACAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTT  >  NZ_CP009273/1695491‑1695627

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑