Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,691	Δ1 bp	pseudogene (8/93 nt)	renD →	DLP12 prophage; protein RenD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,689	0	G	.	100.0%	205.0 / NA	49	pseudogene (6/93 nt)	renD	DLP12 prophage; protein RenD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (16/33);  total (16/33)

GGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCT  >  NC_000913/566559‑566823                                                                                                                                   |                                                                                                                                       ggtgAGACGATACCTCAACCAGGAAGACAACTTCCTGATATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAgg                                                                                                                              <  1:328829/140‑1 (MQ=255) ggtgAGACGATACCTCAACCAGCAACACACCTTCCTGCTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAgg                                                                                                                              <  1:212771/140‑1 (MQ=255)     agaCGATACCTGAACCAATAAAGCAACTTCCGGATCTGGCCGGTAGACGTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAat                                                                                                                          <  2:352020/140‑1 (MQ=255)          aTACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTc                                                                                                                     >  2:513459/1‑140 (MQ=255)           tACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCa                                                                                                                    >  2:432407/1‑140 (MQ=255)                 aaCCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCt                                                                                                              <  1:24864/140‑1 (MQ=255)                     aGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTgggg                                                                                                          <  1:16179/140‑1 (MQ=255)                     aGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTgggg                                                                                                          <  2:472412/140‑1 (MQ=255)                     aGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTgggg                                                                                                          <  1:716033/140‑1 (MQ=255)                      gTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGa                                                                                                         <  2:472685/140‑1 (MQ=255)                      gTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGa                                                                                                         >  1:633847/1‑140 (MQ=255)                       tAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGAc                                                                                                        >  1:86201/1‑140 (MQ=255)                       tAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGAc                                                                                                        >  2:665900/1‑140 (MQ=255)                       tAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGAc                                                                                                        >  1:762803/1‑140 (MQ=255)                       tAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGAc                                                                                                        >  1:755519/1‑140 (MQ=255)                       tAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGAc                                                                                                        <  1:513459/140‑1 (MQ=255)                         aaaCAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGc                                                                                                      <  2:117463/140‑1 (MQ=255)                           acaacTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGACGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCAt                                                                                                    <  2:635851/140‑1 (MQ=255)                                ttCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAagag                                                                                               <  2:633847/140‑1 (MQ=255)                                    tGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTAAGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTc                                                                                           >  2:726770/1‑140 (MQ=255)                                       tATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCtgt                                                                                        <  1:664217/140‑1 (MQ=255)                                          gggCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGca                                                                                     <  1:204833/140‑1 (MQ=255)                                              ggTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAgg                                                                                 >  2:491355/1‑140 (MQ=255)                                              ggTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAgg                                                                                 >  1:712491/1‑140 (MQ=255)                                                    ccTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTg                                                                           <  1:197081/140‑1 (MQ=255)                                                              gTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAAc                                                                 <  2:762803/140‑1 (MQ=255)                                                               tGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACa                                                                >  2:351279/1‑140 (MQ=255)                                                                   caGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGgcg                                                            <  2:668321/140‑1 (MQ=255)                                                                        tctGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAAcc                                                       <  2:755519/140‑1 (MQ=255)                                                                        tctGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAAcc                                                       <  1:515715/140‑1 (MQ=255)                                                                        tctGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAAcc                                                       <  2:86201/140‑1 (MQ=255)                                                                             cGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAAt                                                  <  1:653245/140‑1 (MQ=255)                                                                              gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATc                                                 <  1:351279/140‑1 (MQ=255)                                                                                aGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTg                                               >  2:130174/1‑140 (MQ=255)                                                                                      cAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGGCGTGGCCTCGGTAACAGGCGCCACCGTAATCTGATCTTa                                         >  2:326846/1‑140 (MQ=255)                                                                                      cAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTa                                         >  1:594392/1‑140 (MQ=255)                                                                                           aTTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTCATCTTACCCAg                                    <  2:823722/140‑1 (MQ=255)                                                                                           aTTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTAAGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                    <  1:726770/140‑1 (MQ=255)                                                                                                      gTTCGGACTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGac                         <  1:491355/140‑1 (MQ=255)                                                                                                      gTTCGGACTGAAAGGAGCAAGTCTATGAC‑GGTAAAAAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGac                         <  2:210411/140‑1 (MQ=255)                                                                                                            aCTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATGTTGCCCAGCGATAGTGGACACGCgg                   >  1:210411/1‑140 (MQ=255)                                                                                                            aCTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGac                         <  2:665112/134‑1 (MQ=255)                                                                                                            aCTGAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGac                         >  1:665112/1‑134 (MQ=255)                                                                                                               gAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTa                <  2:712491/140‑1 (MQ=255)                                                                                                               gAAAGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTa                <  2:486332/140‑1 (MQ=255)                                                                                                                aaaGGAGCAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTaa               <  1:407995/140‑1 (MQ=255)                                                                                                                aaaGGAGCAAGTGTACGAC‑GGCTAACAGGTAATTATTTATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTaa               <  1:256225/140‑1 (MQ=38)                                                                                                                       cAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTa        <  1:130174/140‑1 (MQ=255)                                                                                                                       cAAGTGTATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTa        <  2:594392/140‑1 (MQ=255)                                                                                                                             tATGAC‑GGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAActct  <  1:576364/140‑1 (MQ=255)                                                                                                                                   |                                                                                                                                       GGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCT  >  NC_000913/566559‑566823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑