Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,280,999	T→C	pseudogene (299/402 nt)	agaW →	N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,280,999	0	T	C	100.0%	53.7 / NA	17	pseudogene (299/402 nt)	agaW	N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (8/9);  total (8/9)

TGGTGTGGATGGGGCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGTACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGCTGGTGCCGACGGCC  >  NC_000913/3280873‑3281119                                                                                                                               |                                                                                                                         tGGTGTGGATGGGGCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTc                                                                                                             <  2:86849/140‑1 (MQ=255)             ggCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATg                                                                                                 >  1:315643/1‑140 (MQ=255)             ggCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATg                                                                                                 >  1:37476/1‑140 (MQ=255)              gCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATgg                                                                                                >  1:207780/1‑140 (MQ=255)                 ggCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGa                                                                                             <  2:255311/140‑1 (MQ=255)                       gCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCt                                                                                       >  1:168330/1‑140 (MQ=255)                                                 tGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTg                                                             >  1:20781/1‑140 (MQ=255)                                                                tcgtcgGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGc                                                 <  1:332531/137‑1 (MQ=255)                                                                tcgtcgGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGc                                                 >  2:332531/1‑137 (MQ=255)                                                                          ggCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGAc                                              >  2:155218/1‑130 (MQ=255)                                                                          ggCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGAc                                              <  1:155218/130‑1 (MQ=255)                                                                                  ccATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCgcgc                            <  2:333014/140‑1 (MQ=255)                                                                                   cATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGcgcc                           <  2:315643/140‑1 (MQ=255)                                                                                              gCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGc                >  2:212950/1‑140 (MQ=255)                                                                                               cGTGAAACCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGCt               <  2:168330/140‑1 (MQ=255)                                                                                                    aaCCCGATGTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGCTGGTGc          <  2:207780/140‑1 (MQ=255)                                                                                                            gTCGCAGTAGGTGTCGCCGCACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGCTGGTGCCGACGGcc  <  2:37476/140‑1 (MQ=255)                                                                                                                               |                                                                                                                         TGGTGTGGATGGGGCTGGCCCCGCTGGCGGGCGCACAGCCGCCTAACGTGATTATCGGTACTATCGTCGGCACGGCGTTTGCCATTACTACTGGCGTGAAACCCGATGTCGCAGTAGGTGTCGCCGTACCTTTCGCTGTCGCAGTACAGATGGGGATTACCTTCCTGTTCTCGGTGATGTCCGGCGTGATGTCTCGCTGCGACCTGGCAACAAACCCGCGCCGCATTTGATGCTGGTGCCGACGGCC  >  NC_000913/3280873‑3281119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑