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%	159.5 / NA	50	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/28);  total (22/28)

AGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAA  >  NC_000913/239243‑239507                                                                                                                                        |                                                                                                                                  aGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                >  2:1127678/1‑139 (MQ=18) aGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                >  1:973510/1‑139 (MQ=21)      tACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAccc                                                                                                                           >  1:380028/1‑139 (MQ=38)          gCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGAc                                                                                                                       <  2:973510/139‑1 (MQ=255)              aTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACtctc                                                                                                                   >  2:419311/1‑139 (MQ=255)               ttGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTcc                                                                                                                  >  2:1278729/1‑139 (MQ=255)                tGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 <  2:702615/139‑1 (MQ=255)                  cTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                               <  1:419311/139‑1 (MQ=255)                       aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCtt                                                                                                          >  2:1113075/1‑139 (MQ=255)                           ttttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                      <  1:1113075/139‑1 (MQ=255)                             ttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                    <  2:342466/139‑1 (MQ=255)                                  gAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                               <  1:1383488/139‑1 (MQ=255)                                  gAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                               <  1:1127678/139‑1 (MQ=255)                                   aaTGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGTGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 >  2:968458/1‑120 (MQ=255)                                   aaTGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGTGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 <  1:968458/120‑1 (MQ=255)                                     tGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                            <  2:981915/139‑1 (MQ=255)                                           ggTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacc                                                                                      <  2:380028/139‑1 (MQ=255)                                                tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAAc                                                                                 >  1:255170/1‑139 (MQ=255)                                                   aGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAc                                                                                                 <  2:1266511/120‑1 (MQ=255)                                                   aGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAc                                                                                                 >  1:1266511/1‑120 (MQ=255)                                                     gCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTaaa                                                                            <  2:255170/139‑1 (MQ=255)                                                       aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                <  2:737605/85‑1 (MQ=17)                                                       aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                >  1:737605/1‑85 (MQ=17)                                                       aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 <  1:927345/100‑1 (MQ=255)                                                       aGGGATAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 >  2:927345/1‑100 (MQ=255)                                                         ggTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCa                                                                        >  1:676710/1‑139 (MQ=255)                                                              aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGc                                                                   >  1:965193/1‑139 (MQ=255)                                                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                               >  2:1355208/1‑106 (MQ=255)                                                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                               <  1:1355208/106‑1 (MQ=255)                                                                     aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGc                                                            >  2:126883/1‑139 (MQ=255)                                                                      gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAATCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAATACAACGCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                                           <  1:957186/139‑1 (MQ=255)                                                                          cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                          <  1:605921/104‑1 (MQ=255)                                                                          cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                          >  2:605921/1‑104 (MQ=255)                                                                          cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTACACTCATCCGCATCCTGCCATGc                                                       >  2:620979/1‑139 (MQ=255)                                                                           gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGcc                                                      <  2:965193/139‑1 (MQ=255)                                                                              aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGCCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCTTCCGCATCCTGCCATGCCGGa                                                   <  2:861281/139‑1 (MQ=255)                                                                                    ccATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACttt                                             >  2:1169726/1‑139 (MQ=255)                                                                                     cATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                            <  2:1005054/139‑1 (MQ=255)                                                                                        ggACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtctc                                         <  1:1278729/139‑1 (MQ=255)                                                                                              aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                    >  2:1304656/1‑74 (MQ=255)                                                                                              aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                    <  1:1304656/74‑1 (MQ=255)                                                                                                    ccTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 >  2:80021/1‑55 (MQ=255)                                                                                                    ccTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                 <  1:80021/55‑1 (MQ=255)                                                                                                      tGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAt                           >  2:578766/1‑139 (MQ=255)                                                                                                            cAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGcc                     <  1:620979/139‑1 (MQ=255)                                                                                                              gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATcc                                                                     <  2:1421377/89‑1 (MQ=255)                                                                                                              gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATcc                                                                     >  1:1421377/1‑89 (MQ=255)                                                                                                              gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                                 <  2:177444/109‑1 (MQ=255)                                                                                                              gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                                 >  1:177444/1‑109 (MQ=255)                                                                                                                   tGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACa              >  1:1031984/1‑139 (MQ=255)                                                                                                                            cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                               <  2:1199597/97‑1 (MQ=255)                                                                                                                            cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                               >  1:1199597/1‑97 (MQ=255)                                                                                                                             gggCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATc    <  2:1031984/139‑1 (MQ=255)                                                                                                                               gCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCaa  <  1:1169726/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                  AGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAA  >  NC_000913/239243‑239507

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: ‑