Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,808,741	T→C	pseudogene (172/924 nt)	ygaY →	pseudogene, major facilitator transporter superfamily,putative transport, Not classified, putative transport protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,808,741	0	T	C	100.0%	238.6 / NA	66	pseudogene (172/924 nt)	ygaY	pseudogene, major facilitator transporter superfamily,putative transport, Not classified, putative transport protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (32/34);  total (32/34)

TGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAA  >  NC_000913/2808610‑2808875                                                                                                                                    |                                                                                                                                       tgatgatCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGAt                                                                                                                                 <  1:740798/139‑1 (MQ=255)     gatCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                             <  2:1335771/139‑1 (MQ=255)      atCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                             >  2:953126/1‑138 (MQ=255)      atCCTCGGCACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                             <  1:953126/138‑1 (MQ=255)             gTACGGCATTAACCGGTTTAGTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACg                                                                                                                     >  1:948562/1‑139 (MQ=255)               aCGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                   <  2:1613804/139‑1 (MQ=255)                 ggCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                             >  2:686686/1‑127 (MQ=255)                 ggCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                             <  1:686686/127‑1 (MQ=255)                        aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACC‑GATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCgg                                                                                                         >  1:1614929/1‑139 (MQ=255)                             tttCTTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCAGTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACggg                                                                                                                   <  2:991306/125‑2 (MQ=255)                             tttATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                   >  1:991306/1‑125 (MQ=255)                                 ttCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                   >  2:738222/1‑121 (MQ=255)                                 ttCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                   <  1:738222/121‑1 (MQ=255)                                           tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTg                                                                                                                          >  2:422729/1‑104 (MQ=255)                                           tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTg                                                                                                                          <  1:422729/104‑1 (MQ=255)                                           tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcgg                                                                                       >  1:613099/1‑139 (MQ=255)                                            ggCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcggc                                                                                      >  2:1196582/1‑139 (MQ=255)                                             gCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcggcg                                                                                     >  1:307173/1‑139 (MQ=255)                                                     tCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGgcgc                                                                             <  1:1143537/139‑1 (MQ=255)                                                       tGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                           <  2:307173/139‑1 (MQ=255)                                                         gTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGAc                                                                                                                  >  2:1352805/1‑98 (MQ=255)                                                         gTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGAc                                                                                                                  <  1:1352805/98‑1 (MQ=255)                                                         gTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGgcg                                                                              >  2:1217460/1‑134 (MQ=255)                                                         gTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGgcg                                                                              <  1:1217460/134‑1 (MQ=255)                                                             cGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcgg                                                                                       <  2:1612976/121‑1 (MQ=255)                                                             cGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcgg                                                                                       >  1:1612976/1‑121 (MQ=255)                                                              gCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCttt                                                                    <  2:664643/139‑1 (MQ=255)                                                               cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                       >  1:1614839/1‑87 (MQ=255)                                                               cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTgg                                                                                                 >  1:713274/1‑109 (MQ=255)                                                               cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTgg                                                                                                 <  2:713274/109‑1 (MQ=255)                                                               cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCtttt                                                                   >  1:1403534/1‑139 (MQ=255)                                                               cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTAGTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                       <  2:1614839/87‑1 (MQ=255)                                                                    aGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGtt                                                              >  2:832699/1‑139 (MQ=255)                                                                       gACGCTGGCTTCACC‑GATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGAACCGTCTTTTGGGTTGCtt                                                          <  2:1614929/139‑1 (MQ=255)                                                                        aCGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGa                                                                                                        >  2:194537/1‑93 (MQ=255)                                                                        aCGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGa                                                                                                        <  1:194537/93‑1 (MQ=255)                                                                         cGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                           <  1:709261/73‑1 (MQ=255)                                                                         cGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                           >  2:709261/1‑73 (MQ=255)                                                                                   aCCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATg                                               >  2:261630/1‑139 (MQ=255)                                                                                        aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcggc                                                                                      >  2:134764/1‑95 (MQ=255)                                                                                        aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcggc                                                                                      <  1:134764/95‑1 (MQ=255)                                                                                        aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACt                                          >  1:1488363/1‑139 (MQ=255)                                                                                               cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                          <  2:361885/100‑1 (MQ=255)                                                                                               cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                          >  2:92562/1‑100 (MQ=255)                                                                                               cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                          <  1:92562/100‑1 (MQ=255)                                                                                               cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                          >  1:361885/1‑100 (MQ=255)                                                                                                ggCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGgcgc                                  <  1:832699/139‑1 (MQ=255)                                                                                                 gCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAg                                                                                                                >  1:1538831/1‑60 (MQ=255)                                                                                                 gCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAg                                                                                                                <  2:1538831/60‑1 (MQ=255)                                                                                                  cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTg                                <  1:1196582/139‑1 (MQ=255)                                                                                                       tGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCAtt                           <  2:1403534/139‑1 (MQ=255)                                                                                                            ggCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                      <  2:613099/139‑1 (MQ=255)                                                                                                            ggCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGCTAATGGCACTGATGGCGCTGGCATTATGGc                      >  1:1273623/1‑139 (MQ=255)                                                                                                             gCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCg                     <  2:1488363/139‑1 (MQ=255)                                                                                                                 tattatGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGgcg                                   <  1:196151/121‑1 (MQ=255)                                                                                                                 tattatGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGgcg                                   >  2:196151/1‑121 (MQ=255)                                                                                                                       gAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCca           <  2:948562/139‑1 (MQ=255)                                                                                                                           ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCa                             >  2:176976/1‑117 (MQ=255)                                                                                                                           ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCa                             <  1:176976/117‑1 (MQ=255)                                                                                                                           ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACaaa       >  2:334412/1‑139 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCg                                                                                               >  1:1427694/1‑49 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCg                                                                                               <  2:1427694/49‑1 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCtt                                                          >  2:1596494/1‑86 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCtt                                                          <  1:1596494/86‑1 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGAt                                       <  1:1306442/105‑1 (MQ=255)                                                                                                                             tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGAt                                       >  2:1306442/1‑105 (MQ=255)                                                                                                                               tgctgcTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGaa   <  1:261630/139‑1 (MQ=255)                                                                                                                                gctgctGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGaaa  >  2:670249/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                       TGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAA  >  NC_000913/2808610‑2808875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑