Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,540,435	A→T	intergenic (‑150/+110)	yddL ← / ← yddG	porin/aromatic amino acid efflux DMT transporter YddG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,540,435	0	A	T	83.3%	10.3 / ‑2.4	6	intergenic (‑150/+110)	yddL/yddG	porin/aromatic amino acid efflux DMT transporter YddG
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (1/4);  total (2/4)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01

AATGACATACTGTTTTTAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGATCGAAGTCGAAATGAGATATAAGGTGAATTACTGGTATTTGAAATTTATTTTTTTAATA  >  NZ_CP009273/1540353‑1540494                                                                                   |                                                            aaTGACATACTGTTTTTAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGTTCGAAGt                                                      >  2:220884/1‑90 (MQ=255)  aTGACATACTGTTTTTAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGTTCGAAGTc                                                     <  1:473036/90‑1 (MQ=255)        tACTGTTTTTAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGTTCGAAGTCGAAATg                                               <  1:268488/90‑1 (MQ=255)              ttttAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGTTCGAAGTCGAAATGAGatat                                         <  1:441057/90‑1 (MQ=255)               tttAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGATCGAAGTCGAAATGAGAtata                                        >  1:255323/1‑90 (MQ=255)                                                     aGATGAAATAATATTATTTATCGATATGTGTTCGAAGTCGAAATGAGATATAAGGTGAATTACTGGTATTTGAAATTTATTTTTTTAata  <  2:270067/90‑1 (MQ=255)                                                                                   |                                                            AATGACATACTGTTTTTAAAATAGAATGGTGATTAAAAACAATGAGAAAAATAGATGAAATAATATTATTTATCGATATGTGATCGAAGTCGAAATGAGATATAAGGTGAATTACTGGTATTTGAAATTTATTTTTTTAATA  >  NZ_CP009273/1540353‑1540494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑