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%	138.8 / 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 (23/22);  total (23/22)

ACTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAT  >  NC_000913/1425845‑1426114                                                                                                                                        |                                                                                                                                       aCTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTg                                                                                                                                     <  2:824531/139‑1 (MQ=255)    ggAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                   >  2:809416/1‑138 (MQ=255)    ggAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAACATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGcc                                                                                                                                   <  1:809416/138‑1 (MQ=255)               cAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTa                                                                                                                       >  1:87931/1‑139 (MQ=255)                aGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTAt                                                                                                                      <  2:1471426/139‑1 (MQ=255)                  aaCGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCg                                                                                                                    >  2:713263/1‑139 (MQ=255)                                 tgctTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGaa                                                                                                     >  2:343688/1‑139 (MQ=255)                                          aGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaa                                                                                            <  2:52162/139‑1 (MQ=255)                                             aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                              >  2:1168389/1‑118 (MQ=255)                                             aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTc                                                                                                              <  1:1168389/118‑1 (MQ=255)                                                        tACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGaa                                                                              >  1:1184851/1‑139 (MQ=255)                                                        tACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGaa                                                                              >  1:1201396/1‑139 (MQ=255)                                                             gCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCgag                                                                         <  2:285801/139‑1 (MQ=255)                                                              cAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCgaga                                                                        >  2:1178679/1‑139 (MQ=255)                                                                gATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                              <  2:699390/83‑1 (MQ=255)                                                                gATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCg                                                                                                                              >  1:699390/1‑83 (MQ=255)                                                                  tCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGGTAAAAAAGCCATAACTGCCCAGCGGCGGTTATCGGAGTTAGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGaaaaa                                                                    >  2:72223/1‑139 (MQ=255)                                                                             gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGcc                                                         >  1:662247/1‑139 (MQ=255)                                                                                gccagcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATg                                                                                 <  2:1145012/112‑1 (MQ=255)                                                                                gccagcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATg                                                                                 >  1:1145012/1‑112 (MQ=255)                                                                                gccagcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCAcc                                                      <  1:343688/139‑1 (MQ=255)                                                                                     cATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                        >  1:754593/1‑100 (MQ=255)                                                                                     cATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                        <  2:754593/100‑1 (MQ=255)                                                                                     cATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATAc                                                 >  1:970337/1‑139 (MQ=255)                                                                                       tCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                               <  2:1184851/139‑1 (MQ=255)                                                                                       tCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                               <  2:970337/139‑1 (MQ=255)                                                                                       tCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                               <  1:713263/139‑1 (MQ=255)                                                                                              gggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTg                                                           <  1:293302/120‑1 (MQ=255)                                                                                              gggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGATACCGGAGTTCGGGGGAGCAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTg                                                           >  2:293302/1‑120 (MQ=255)                                                                                               ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                        >  2:126818/1‑90 (MQ=255)                                                                                               ggTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAgg                                                                                        <  1:126818/90‑1 (MQ=255)                                                                                                        cagcagAAGCAGGATACGATAAAAAAGCCATAACGGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                              <  1:1178679/139‑1 (MQ=255)                                                                                                                  aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACt                                                                  >  1:668752/1‑93 (MQ=255)                                                                                                                  aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACt                                                                  <  2:668752/93‑1 (MQ=255)                                                                                                                  aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                              >  1:1212119/1‑129 (MQ=255)                                                                                                                  aGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                              <  2:1212119/129‑1 (MQ=255)                                                                                                                     aTACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAg                 <  1:1121081/139‑1 (MQ=255)                                                                                                                     aTACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAg                 >  2:576614/1‑139 (MQ=255)                                                                                                                          aTAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaaa                                                                                           <  1:475986/60‑1 (MQ=255)                                                                                                                          aTAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGaaa                                                                                           >  2:475986/1‑60 (MQ=255)                                                                                                                              aaaaGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTAc        >  1:694899/1‑139 (MQ=255)                                                                                                                                   ccATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTa   <  2:662247/139‑1 (MQ=255)                                                                                                                                    cATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAt  >  2:1336771/1‑139 (MQ=255)                                                                                                                                     aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                               <  1:1216197/93‑1 (MQ=255)                                                                                                                                     aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                               >  2:1216197/1‑93 (MQ=255)                                                                                                                                        |                                                                                                                                       ACTGGAATATACGGCAGAACGAGGGATCGCGCTGCTTAAGCAGAATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAT  >  NC_000913/1425845‑1426114

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑