Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,280,706	A→G	pseudogene (6/402 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	3,280,706	0	A	G	100.0%	107.6 / NA	31	pseudogene (6/402 nt)	agaW	N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/15);  total (16/15)

TGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCA  >  NC_000913/3280629‑3280783                                                                              |                                                                              tGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATc                                                                            <  2:552093/81‑1 (MQ=255) tGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATc                                                                            <  1:552093/81‑1 (MQ=255)       gCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTg                                                                      >  1:552132/1‑81 (MQ=255)             ttCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAg                                                                <  2:552094/81‑1 (MQ=255)               cAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAgg                                                               >  2:552132/1‑80 (MQ=255)                   gCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCAttt                                                          <  1:552096/81‑1 (MQ=255)                     gTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGc                                                        >  1:552150/1‑81 (MQ=255)                       cccGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGt                                                      >  1:552137/1‑81 (MQ=255)                             agagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCa                                                >  2:552133/1‑81 (MQ=255)                             agagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCa                                                >  2:552137/1‑81 (MQ=255)                             agagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCa                                                >  1:552142/1‑81 (MQ=255)                              gagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCAt                                               >  2:552135/1‑81 (MQ=255)                              gagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCAt                                               <  1:552097/81‑1 (MQ=255)                                 ccTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTAt                                            >  1:552153/1‑81 (MQ=255)                                  ctgctgTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATc                                           >  1:552139/1‑81 (MQ=255)                                  ctgctgTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATc                                           <  2:552097/81‑1 (MQ=255)                                  ctgctgTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATc                                           <  1:552099/81‑1 (MQ=255)                                       gtgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCtt                                      >  1:552154/1‑81 (MQ=255)                                        tgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCt                                       <  2:552100/79‑1 (MQ=255)                                        tgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCt                                       <  1:552100/79‑1 (MQ=255)                                          gACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTAt                                   <  2:552101/81‑1 (MQ=255)                                          gACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTAt                                   >  2:552147/1‑81 (MQ=255)                                                tttAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTgg                             >  1:552156/1‑81 (MQ=255)                                                             gAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGtt                 <  1:552103/80‑1 (MQ=255)                                                                 gATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACg            <  1:552104/81‑1 (MQ=255)                                                                     catcatGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGcc         <  1:552105/80‑1 (MQ=255)                                                                      atcatGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCt        <  2:552105/80‑1 (MQ=255)                                                                        catGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAAc     >  2:552157/1‑81 (MQ=255)                                                                         atGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAAcc    <  2:552106/81‑1 (MQ=255)                                                                           ggAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCa  >  1:552145/1‑81 (MQ=255)                                                                           ggAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCa  >  2:552154/1‑81 (MQ=255)                                                                              |                                                                              TGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCA  >  NC_000913/3280629‑3280783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑