Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,878,490	T→C	pseudogene (1082/1482 nt)	yeaV →	BCCT family transporter YeaV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,878,490	0	T	C	100.0%	51.3 / NA	16	pseudogene (1082/1482 nt)	yeaV	BCCT family transporter YeaV
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/10);  total (6/10)

ATCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG  >  NZ_CP009273/1878405‑1878549                                                                                      |                                                            aTCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTc                                                         <  2:323448/90‑1 (MQ=255)                      gAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGtgatg                                    <  1:342020/90‑1 (MQ=255)                      gAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGtgatg                                    <  2:106315/90‑1 (MQ=255)                          cacTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGatta                                >  1:238011/1‑90 (MQ=255)                             tGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTAttt                             >  2:172908/1‑90 (MQ=255)                                             tGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCatat             >  2:394237/1‑90 (MQ=255)                                                aCAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGa          <  2:37498/90‑1 (MQ=255)                                                     aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  1:266490/90‑1 (MQ=255)                                                     aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  2:111961/90‑1 (MQ=255)                                                     aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  2:125100/90‑1 (MQ=255)                                                     aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  2:18741/90‑1 (MQ=255)                                                     aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  2:238011/90‑1 (MQ=255)                                                        ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTgg  >  1:56326/1‑90 (MQ=255)                                                        ttCTAATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTgg  >  1:9717/1‑90 (MQ=255)                                                          cTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     <  1:131051/85‑1 (MQ=255)                                                          cTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg     >  2:131051/1‑85 (MQ=255)                                                                                      |                                                            ATCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG  >  NZ_CP009273/1878405‑1878549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑