Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	276,800	0	A	C	54.5%	6.8 / 11.0	11	Y299D (TAT→GAT)	yagA	IS481‑like element ISEc19 family transposase
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAA  >  NZ_CP009273/276721‑276847                                                                                |                                                tCCTCTTTCCTGACCATCACCCCTCCATCGTTCTCCGGGGGCGTTGTGTTGCCGCTGTAATCCCGCGCTGACGGCTGATCCCGCGAGccc                                       <  2:68508/90‑1 (MQ=255)      tttCCTGCCCACCCCCCCTTCATCTTATCCGGGGGGCGTTGTGTTCCCGCTGTACTCCCGCGCTGACGGCTGATCCCGCGAGCCCGGTAc                                  <  2:421567/90‑1 (MQ=255)      ttcccTGACCCTCCCCCCTTCATCGTTTTCGGGGGGCTTTGTGTTGCCCCTGTCCTCCCGCGCTGACGGCTGATCCCGCGACCCCGGTAc                                  <  2:243895/87‑1 (MQ=255)               cATCACCCCTTCATCGTATTCCGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATc                         >  1:181702/1‑90 (MQ=255)                 tCACCCCTTCATCGTATTCCGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCa                       >  1:417019/1‑90 (MQ=255)                       cTTCATCGTTTCCGGGGGGGGTTGTGTTCCCGCTGTCCGCCCGCGCTGCGGGCTGATCCCGCGACCCCGGTACCGCCATATCCAGCGCCt                 <  2:417019/90‑1 (MQ=255)                                aTTCCGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGc        >  1:346577/1‑90 (MQ=255)                                    cGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTc    <  1:16307/90‑1 (MQ=255)                                      ggggTGTTTTGTTGCCGCTGTCCTGCCGCGCTGACGCCTAACCCCGCGGCCCGGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCaa  <  2:346577/90‑1 (MQ=255)                                                        tGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCa                             >  1:128963/1‑45 (MQ=255)                                                        tGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCa                             <  2:128963/45‑1 (MQ=255)                                                                                |                                                TCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCGTTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAA  >  NZ_CP009273/276721‑276847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑