Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,425,980	G→A	pseudogene (351/453 nt)	ydaY →	pseudogene, Rac prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,425,980	0	G	A	100.0%	143.1 / NA	45	pseudogene (351/453 nt)	ydaY	pseudogene, Rac prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/19);  total (26/19)

TGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATT  >  NC_000913/1425847‑1426115                                                                                                                                      |                                                                                                                                        ttgAATATACGGCAGAACGAGGGATCGCGGCGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAAGGTAAAGGGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    <  1:649442/137‑1 (MQ=255)             cAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGTCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                               <  2:360073/132‑1 (MQ=255)             cAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGTCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                               >  1:360073/1‑132 (MQ=255)                     gggATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                <  1:753604/139‑1 (MQ=255)                            cgcTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    <  2:706836/112‑1 (MQ=255)                            cgcTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    >  1:706836/1‑112 (MQ=255)                            cgcTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGga                                                                                                         >  1:772742/1‑139 (MQ=255)                               tgctTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGTCCAGCGGTGGTTATCGGAGtt                                                                                                                >  1:1396886/1‑129 (MQ=255)                               tgctTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                <  2:1396886/129‑1 (MQ=255)                                  ttAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAgg                                                                                                   >  1:209019/1‑139 (MQ=255)                                          aaTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaaaa                                                                                           >  2:786302/1‑139 (MQ=255)                                           aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAg                                                                                          >  1:1077598/1‑139 (MQ=255)                                                      tACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                               <  1:622706/107‑1 (MQ=255)                                                      tACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                               >  2:622706/1‑107 (MQ=255)                                                        cTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGc                                                                             <  1:341164/139‑1 (MQ=255)                                                             aGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGaa                                                                        >  1:1590961/1‑139 (MQ=255)                                                                tCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    <  2:265528/76‑1 (MQ=255)                                                                tCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    >  1:265528/1‑76 (MQ=255)                                                                 ccTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAAc                                                                    >  2:23192/1‑139 (MQ=255)                                                                     gCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAg                                                                >  2:291417/1‑139 (MQ=255)                                                                           gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACt                                                                   <  1:199381/130‑1 (MQ=255)                                                                           gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACt                                                                   >  2:199381/1‑130 (MQ=255)                                                                           gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGcc                                                          >  1:1239906/1‑139 (MQ=255)                                                                                             ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAg                                                                                                                                 >  1:1600632/1‑50 (MQ=255)                                                                                             ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAg                                                                                                                                 <  2:1600632/50‑1 (MQ=255)                                                                                             ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGa                                        >  2:246062/1‑139 (MQ=255)                                                                                                  agagCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAg                                   >  2:77928/1‑139 (MQ=255)                                                                                                      cagcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                               <  1:246062/139‑1 (MQ=255)                                                                                                       agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  2:684100/1‑139 (MQ=255)                                                                                                       agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  1:499011/1‑139 (MQ=255)                                                                                                        gcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCgg                             >  2:351091/1‑139 (MQ=255)                                                                                                         cagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGaa                                                                                                      >  1:1243477/1‑65 (MQ=255)                                                                                                         cagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGaa                                                                                                      <  2:1243477/65‑1 (MQ=255)                                                                                                                aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAg                     <  1:77928/139‑1 (MQ=255)                                                                                                                   aTACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAcc                                <  1:34927/125‑1 (MQ=255)                                                                                                                   aTACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAcc                                >  2:34927/1‑125 (MQ=255)                                                                                                                      cGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgttg               >  1:620715/1‑139 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaa                                                                                             >  1:1317597/1‑58 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaa                                                                                             <  2:1317597/58‑1 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATAc                                                  <  2:580234/101‑1 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATAc                                                  >  1:580234/1‑101 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgt                 <  2:1573797/134‑1 (MQ=255)                                                                                                                         tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgt                 >  1:1573797/1‑134 (MQ=255)                                                                                                                              aaGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGc       <  1:291417/139‑1 (MQ=255)                                                                                                                                   aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt  <  1:351091/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                        TGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATT  >  NC_000913/1425847‑1426115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑