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%	141.4 / NA	41	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 (19/22);  total (19/22)

GAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCA  >  NC_000913/3280631‑3280783                                                                            |                                                                              gAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAg                                                                          <  1:614211/81‑1 (MQ=255)  aaTGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGc                                                                         >  2:614284/1‑81 (MQ=255)  aaTGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGc                                                                         <  2:614212/81‑1 (MQ=255)          gTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGc                                                                  <  1:614213/80‑1 (MQ=255)             cAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAgg                                                               >  2:614264/1‑80 (MQ=255)              aGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGc                                                              <  1:614214/80‑1 (MQ=255)               gggCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCAt                                                            <  1:614215/81‑1 (MQ=255)                 gCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCAttt                                                          <  1:614216/81‑1 (MQ=255)                  cGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTg                                                         <  1:614218/81‑1 (MQ=255)                  cGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTg                                                         <  2:614217/81‑1 (MQ=255)                   gTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGc                                                        >  2:614255/1‑81 (MQ=255)                      ccGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGt                                                      <  2:614219/80‑1 (MQ=255)                       cGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGAGTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTg                                                    <  2:614220/81‑1 (MQ=255)                         aCAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTggg                                                  >  1:614262/1‑81 (MQ=255)                            gagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCAt                                               >  2:614253/1‑81 (MQ=255)                            gagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCAt                                               <  2:614222/81‑1 (MQ=255)                            gagCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCAt                                               <  1:614221/81‑1 (MQ=255)                                  gctgTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGc                                         >  1:614274/1‑81 (MQ=255)                                  gctgTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGc                                         >  2:614269/1‑81 (MQ=255)                                     gtgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCtt                                      >  2:614268/1‑81 (MQ=255)                                     gtgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCtt                                      >  2:614272/1‑81 (MQ=255)                                      tgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCtt                                      <  1:614223/80‑1 (MQ=255)                                      tgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCtt                                      >  1:614261/1‑80 (MQ=255)                                       ggACCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTa                                    >  1:614263/1‑81 (MQ=255)                                         aCCTCTTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATc                                  >  2:614259/1‑81 (MQ=255)                                            tctTTAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCt                               >  1:614279/1‑81 (MQ=255)                                              tttAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCt                               <  1:614224/79‑1 (MQ=255)                                                tAAATTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTg                              <  1:614225/78‑1 (MQ=255)                                                 aaaTTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGcc                           <  2:614226/80‑1 (MQ=255)                                                  aaTTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTg                         <  2:614227/81‑1 (MQ=255)                                                   aTTACTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTgg                        <  1:614228/81‑1 (MQ=255)                                                      aCTTTGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGata                     >  1:614291/1‑81 (MQ=255)                                                          tGAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGtt                 >  1:614273/1‑81 (MQ=255)                                                           gAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGtt                 >  2:614238/1‑80 (MQ=255)                                                           gAGGGATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGtt                 <  1:614229/80‑1 (MQ=255)                                                             gggATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTaa              <  1:614230/81‑1 (MQ=255)                                                              ggATTCATCATGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAAc             <  2:614231/81‑1 (MQ=255)                                                                  tcatcaTGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGcc         >  2:614276/1‑81 (MQ=255)                                                                    atcatGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTa       <  2:614232/81‑1 (MQ=255)                                                                      catGGAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAAc     >  2:614258/1‑81 (MQ=255)                                                                         ggAGATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCa  >  2:614285/1‑81 (MQ=255)                                                                            |                                                                              GAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCA  >  NC_000913/3280631‑3280783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑