Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	239,378	G→A	pseudogene (273/273 nt)	yafF →	pseudogene, H repeat‑associated protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	239,378	0	G	A	100.0%	124.4 / NA	40	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/22);  total (18/22)

AGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATGCGCG  >  NC_000913/239243‑239513                                                                                                                                        |                                                                                                                                        aGGAATAAGGCAAATTGCTATTAATAATTTGACGAATGAGAAGCAATTCAAGGCAGAGTTAAGACGCAAGACGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCATTGCGGGGAGCAGGCTTTCGtaataa                                                                                                                                      <  2:676984/139‑1 (MQ=11)              aTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcccc                                                                                                                                <  2:373588/132‑1 (MQ=255)              aTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcccc                                                                                                                                >  1:373588/1‑132 (MQ=255)               ttGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcccc                                                                                                                                >  2:231801/1‑131 (MQ=255)               ttGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcccc                                                                                                                                <  1:231801/131‑1 (MQ=255)                tGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                       >  1:749711/1‑139 (MQ=255)                  cTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                                     <  1:1006983/139‑1 (MQ=255)                            tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAaca                                                                                                           >  2:284763/1‑139 (MQ=255)                                   aaTGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAcccc                                                                                                    <  1:1030850/139‑1 (MQ=255)                                       agaAGGAATTCAAGGCAGGGTGAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTGAGTCCTTGCGGGGAGCGGGCTTTCGAAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                                <  2:625895/139‑1 (MQ=18)                                           ggTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacc                                                                                            <  1:284763/139‑1 (MQ=255)                                               ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACaa                                                                                        >  2:1059416/1‑139 (MQ=255)                                                    ggCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTa                                                                                                               >  1:923928/1‑111 (MQ=255)                                                    ggCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTa                                                                                                               <  2:923928/111‑1 (MQ=255)                                                       aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACt                                                                                >  1:1024455/1‑139 (MQ=255)                                                              aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                           >  1:194934/1‑121 (MQ=255)                                                              aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                           <  2:194934/121‑1 (MQ=255)                                                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                          <  1:280217/117‑1 (MQ=255)                                                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                          >  2:280217/1‑117 (MQ=255)                                                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCt                                                                    >  2:619214/1‑139 (MQ=255)                                                                    aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                              >  1:1034410/1‑80 (MQ=255)                                                                    aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                              <  2:1034410/80‑1 (MQ=255)                                                                                ccagcCATGCACACAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCTTAATAATACCCCTACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                                       <  2:578732/138‑1 (MQ=38)                                                                                     cATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                                     >  1:839442/1‑136 (MQ=255)                                                                                     cATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                                     <  2:839442/136‑1 (MQ=255)                                                                                      aTGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtc                                                 <  2:749711/139‑1 (MQ=255)                                                                                       tGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                          >  2:942827/1‑81 (MQ=255)                                                                                       tGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                          <  1:942827/81‑1 (MQ=255)                                                                                        ggACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtctc                                               <  1:18815/139‑1 (MQ=255)                                                                                              aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATAtt                                         <  1:1059416/139‑1 (MQ=255)                                                                                                aCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                           >  2:547152/1‑87 (MQ=255)                                                                                                aCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                           <  1:547152/87‑1 (MQ=255)                                                                                                    ccTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCa                                   >  1:784682/1‑139 (MQ=255)                                                                                                       ggCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg                                <  2:652891/139‑1 (MQ=255)                                                                                                        gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                                     <  2:557368/53‑1 (MQ=255)                                                                                                        gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                                     >  1:557368/1‑53 (MQ=255)                                                                                                          gTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtgctg                             >  2:1011011/1‑139 (MQ=255)                                                                                                            cAGTCCTCCCGGGGCGCGGGCTTTCGTAATAATCCCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCAGCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGcc                           <  2:693440/139‑1 (MQ=255)                                                                                                                  ttGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAc                     <  1:1011011/139‑1 (MQ=255)                                                                                                                            cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                                     >  1:925577/1‑49 (MQ=255)                                                                                                                            cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                                     <  2:925577/49‑1 (MQ=255)                                                                                                                                     gtaataATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATGcgcg  <  2:784682/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                        AGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATGCGCG  >  NC_000913/239243‑239513

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑