Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,215,948	T→C	pseudogene (487/2243 nt)	BW25113_RS25990 →	autotransporter outer membrane beta‑barrel domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,215,948	0	T	C	100.0%	22.1 / NA	8	pseudogene (487/2243 nt)	BW25113_RS25990	autotransporter outer membrane beta‑barrel domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/5);  total (3/5)

AACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAC  >  NZ_CP009273/1215861‑1216029                                                                                        |                                                                                  aaCATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTccc                                                                                 <  1:26321/90‑1 (MQ=255)        atatAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCa                                                                          >  2:268929/1‑90 (MQ=255)             aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg                                                                     <  2:107714/90‑1 (MQ=255)                                           aaaGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAAtt                                       <  1:25444/90‑1 (MQ=255)                                               cccccATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATg                                   <  1:178038/90‑1 (MQ=255)                                                                       gtggAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCa           >  2:318204/1‑90 (MQ=255)                                                                           agagTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAAt       <  2:64789/90‑1 (MQ=255)                                                                                tATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAc  <  1:318204/90‑1 (MQ=255)                                                                                tATTTTTTCCAAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAc  >  2:353750/1‑90 (MQ=255)                                                                                        |                                                                                  AACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAC  >  NZ_CP009273/1215861‑1216029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑