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%	186.1 / NA	53	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 (27/26);  total (27/26)

GCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATG  >  NC_000913/2808606‑2808872                                                                                                                                        |                                                                                                                                    gCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTgg                                                                                                                                  <  2:149523/139‑1 (MQ=255)         gatCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  1:277149/1‑139 (MQ=255)                   aCGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:700395/139‑1 (MQ=255)                   aCGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:519413/139‑1 (MQ=255)                       cATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            >  1:400938/1‑139 (MQ=255)                            aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                    >  2:311496/1‑126 (MQ=255)                            aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                    <  1:311496/126‑1 (MQ=255)                                          aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                        <  1:243783/108‑1 (MQ=255)                                          aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                        >  2:243783/1‑108 (MQ=255)                                          aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  2:726070/1‑116 (MQ=255)                                          aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:726070/116‑1 (MQ=255)                                           gTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            <  2:1367617/119‑1 (MQ=255)                                           gTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            >  1:1367617/1‑119 (MQ=255)                                               tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  2:230560/1‑101 (MQ=255)                                               tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          <  1:230560/101‑1 (MQ=255)                                                      aaTTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTgg                                                                             >  1:161406/1‑139 (MQ=255)                                                          cTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCa                                                                         >  2:728505/1‑139 (MQ=255)                                                                ccGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCt                                                                   >  1:510054/1‑139 (MQ=255)                                                                       cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTggga                                                            >  2:124379/1‑138 (MQ=255)                                                                       cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGt                                                            <  2:1063634/139‑1 (MQ=255)                                                                       cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGATCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGt                                                            <  1:373485/139‑1 (MQ=255)                                                                          cGACGCTGACTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGc                                                         >  2:1257556/1‑139 (MQ=255)                                                                            aCGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCtt                                                       <  1:728505/139‑1 (MQ=255)                                                                             cGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTc                                                      <  2:277149/139‑1 (MQ=255)                                                                              gCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCTGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCg                                                     <  1:124379/139‑1 (MQ=255)                                                                                tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGa                                                                                                                               <  1:704424/63‑1 (MQ=255)                                                                                tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGa                                                                                                                               >  2:704424/1‑63 (MQ=255)                                                                                tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:544107/78‑1 (MQ=255)                                                                                tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  2:544107/1‑78 (MQ=255)                                                                                    ttCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  1:883206/1‑64 (MQ=255)                                                                                    ttCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          <  2:883206/64‑1 (MQ=255)                                                                                      cACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAAt                                             >  1:407784/1‑139 (MQ=255)                                                                                       aCCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGcc                                                                                                        <  2:407063/79‑1 (MQ=255)                                                                                       aCCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGcc                                                                                                        >  1:407063/1‑79 (MQ=255)                                                                                            aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        >  2:439265/1‑106 (MQ=255)                                                                                            aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        <  1:439265/106‑1 (MQ=255)                                                                                            aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACt                                       >  1:1468162/1‑139 (MQ=255)                                                                                             tAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTg                                      <  2:400938/139‑1 (MQ=255)                                                                                                aCGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATg                                   >  2:1401507/1‑139 (MQ=255)                                                                                                      cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  2:1179563/56‑1 (MQ=255)                                                                                                      cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  1:1179563/1‑56 (MQ=255)                                                                                                                ggCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   <  1:1401507/139‑1 (MQ=255)                                                                                                                     tattatGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGt              <  2:407784/139‑1 (MQ=255)                                                                                                                            aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        >  1:916120/1‑74 (MQ=255)                                                                                                                            aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   >  2:1437398/1‑127 (MQ=255)                                                                                                                            aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   <  1:1437398/127‑1 (MQ=255)                                                                                                                            aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATCGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        <  2:916120/74‑1 (MQ=255)                                                                                                                               ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                       >  1:795892/1‑72 (MQ=255)                                                                                                                               ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                       <  2:795892/72‑1 (MQ=255)                                                                                                                                 tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCg                  <  2:817505/123‑1 (MQ=255)                                                                                                                                 tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGATTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCg                  >  1:817505/1‑123 (MQ=255)                                                                                                                                 tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGATGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTGTGGCGTGGTCTGCCACAAATg  >  2:164676/1‑139 (MQ=255)                                                                                                                                 tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTGTGGGTTGCTTCGGTGTTGATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATg  >  2:987749/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                    GCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATG  >  NC_000913/2808606‑2808872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑