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%	171.8 / NA	55	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 (28/27);  total (28/27)

ACTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATT  >  NC_000913/1425845‑1426115                                                                                                                                        |                                                                                                                                        aCTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAACCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTg                                                                                                                                      >  2:957312/1‑139 (MQ=255)  cTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGc                                                                                                                                     <  2:617313/139‑1 (MQ=255)      aaTATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAg                                                                                                                                 <  2:214967/139‑1 (MQ=255)        tataCGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                               <  1:992852/139‑1 (MQ=255)               cAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                               >  2:154669/1‑132 (MQ=255)               cAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                               <  1:154669/132‑1 (MQ=255)                  aaCGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                     >  2:874056/1‑139 (MQ=255)                    cGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTCGTTATAGGa                                                                                                                   >  2:633585/1‑139 (MQ=255)                         gATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    >  1:616875/1‑117 (MQ=255)                         gATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTGGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                    <  2:616875/117‑1 (MQ=255)                                ctgctTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAACCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGgaga                                                                                                       <  1:957312/139‑1 (MQ=255)                                        gCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAgggggg                                                                                               <  2:173710/139‑1 (MQ=255)                                             aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                >  1:1064505/1‑117 (MQ=255)                                             aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                <  2:1064505/117‑1 (MQ=255)                                                   agTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGa                                                                                    >  2:735775/1‑139 (MQ=255)                                                      tGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATgg                                                                                 >  1:445072/1‑139 (MQ=255)                                                             gCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCgag                                                                          >  1:31607/1‑139 (MQ=255)                                                               aGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                     >  1:917591/1‑94 (MQ=255)                                                               aGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                     <  2:917591/94‑1 (MQ=255)                                                                          gAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGtt                                                             <  2:1072473/139‑1 (MQ=255)                                                                            agcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAgg                                                               >  1:317249/1‑135 (MQ=255)                                                                            agcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAgg                                                               <  2:317249/135‑1 (MQ=255)                                                                             gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                     <  1:663453/80‑1 (MQ=255)                                                                             gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                     >  2:663453/1‑80 (MQ=255)                                                                                 ccagcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCg                                                      >  2:271339/1‑139 (MQ=255)                                                                                       tCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                <  1:904783/75‑1 (MQ=255)                                                                                       tCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGtt                                                                                                                >  2:904783/1‑75 (MQ=255)                                                                                           ccAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                            <  2:445072/139‑1 (MQ=255)                                                                                               ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                               <  1:929934/68‑1 (MQ=255)                                                                                               ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                               >  2:929934/1‑68 (MQ=255)                                                                                               ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGa                                        >  1:628627/1‑139 (MQ=255)                                                                                                    agagCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                         <  2:211553/85‑1 (MQ=255)                                                                                                    agagCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                         >  1:211553/1‑85 (MQ=255)                                                                                                    agagCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                            <  2:532339/130‑1 (MQ=255)                                                                                                    agagCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                            >  1:532339/1‑130 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  2:1014762/1‑139 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              <  2:905967/139‑1 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  1:1014411/1‑139 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  1:215397/1‑139 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCg                              >  1:32003/1‑139 (MQ=255)                                                                                                         agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGAGGTTATTGGAGTTCTGGGGAGAAAGGGGGGAAAAAGCAGAATGGCAGCGAGAAAAACTCAGGGTACAACCGCTACCGCAACTAGAAATatgccgg                              >  2:212603/1‑133 (MQ=255)                                                                                                          gcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGTTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCgg                             >  2:758442/1‑139 (MQ=255)                                                                                                           cagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGt                            >  1:613322/1‑139 (MQ=255)                                                                                                                gCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTa                       >  1:669326/1‑139 (MQ=255)                                                                                                                 cAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                               <  2:541758/130‑1 (MQ=255)                                                                                                                 cAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                               >  1:541758/1‑130 (MQ=255)                                                                                                                  aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAg                     <  1:874056/139‑1 (MQ=255)                                                                                                                     aTACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAg                  <  2:31607/139‑1 (MQ=255)                                                                                                                          aTAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgttgtt             >  2:1057787/1‑139 (MQ=255)                                                                                                                                aaGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGc       <  1:605379/139‑1 (MQ=255)                                                                                                                                aaGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGAACGc       <  1:1014762/139‑1 (MQ=255)                                                                                                                                   ccATAACTGCCCAGCGGTGGTGATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTa    <  1:633585/139‑1 (MQ=255)                                                                                                                                     aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt  <  1:244592/139‑1 (MQ=255)                                                                                                                                     aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt  <  1:735775/139‑1 (MQ=255)                                                                                                                                     aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt  <  2:283967/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                        ACTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATT  >  NC_000913/1425845‑1426115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑