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%	199.2 / NA	61	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/31);  total (30/31)

CACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCG  >  NC_000913/239253‑239501                                                                                                                              |                                                                                                                            cacaTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                  <  1:966413/137‑1 (MQ=255) cacaTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                  >  2:966413/1‑137 (MQ=255)           ttAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTcc                                                                                                      >  2:276733/1‑139 (MQ=255)             aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCtt                                                                                                    >  1:174145/1‑139 (MQ=255)                  tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAaca                                                                                               <  2:174145/139‑1 (MQ=255)                             agaAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                    <  1:1135032/139‑1 (MQ=255)                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                         >  1:605550/1‑110 (MQ=255)                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                         <  2:605550/110‑1 (MQ=255)                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                <  2:1102430/119‑1 (MQ=255)                                     ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                >  1:1102430/1‑119 (MQ=255)                                                    aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGc                                                             >  1:909993/1‑139 (MQ=255)                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                          <  2:810640/73‑1 (MQ=17)                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                          >  1:810640/1‑73 (MQ=9)                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              >  1:1568752/1‑101 (MQ=255)                                                         tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              <  2:1568752/101‑1 (MQ=255)                                                           aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcc                                                                                                                      >  2:435160/1‑75 (MQ=255)                                                           aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcc                                                                                                                      <  1:435160/75‑1 (MQ=255)                                                               gCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                         >  1:1107097/1‑84 (MQ=255)                                                               gCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                         <  2:1107097/84‑1 (MQ=255)                                                                 gAAAAGCAGCCACGGACAGAAACTACCTGGCGTCAGTCCTTGTGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                      >  2:68616/1‑101 (MQ=255)                                                                 gAAAAGCAGCCACGGACAGAAACTACCTGGCGTCAGTCCTTGTGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                      <  1:68616/101‑1 (MQ=255)                                                                 aaaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCGTAATAATACCCCGAGTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGcc                                                >  1:1039987/2‑139 (MQ=255)                                                                    aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGa                                             <  2:780239/139‑1 (MQ=255)                                                                      gcagcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           <  1:1440111/139‑1 (MQ=255)                                                                        agcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCTGGGAGCGGGCGTTCGTAATAATACCCAGACTCTCCCCGTCCTTAAACAC‑ACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtt                                        >  1:1076876/1‑139 (MQ=38)                                                                         gcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                >  2:907707/1‑83 (MQ=255)                                                                         gcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAac                                                                                                <  1:907707/83‑1 (MQ=255)                                                                          ccATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACttt                                       >  2:1236753/1‑139 (MQ=255)                                                                            aTGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtc                                     >  1:1446614/1‑139 (MQ=255)                                                                             tGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                  >  1:559139/1‑61 (MQ=255)                                                                             tGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGa                                                                                                                  <  2:559139/61‑1 (MQ=255)                                                                                   gAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTatat                              <  2:1446614/139‑1 (MQ=255)                                                                                         aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                           >  1:1106002/1‑56 (MQ=255)                                                                                         aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                           <  2:1106002/56‑1 (MQ=255)                                                                                         aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                            <  2:1510251/103‑1 (MQ=255)                                                                                         aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                            >  1:1510251/1‑103 (MQ=255)                                                                                             ggCGTCAGTCCTTGCGGGGAGCGGGCTGTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg                    <  1:661148/139‑1 (MQ=255)                                                                                              gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                      >  2:731506/1‑120 (MQ=255)                                                                                              gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                      <  1:731506/120‑1 (MQ=255)                                                                                               cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           <  1:1621752/114‑1 (MQ=255)                                                                                               cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           <  2:522936/114‑1 (MQ=255)                                                                                               cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           >  1:522936/1‑114 (MQ=255)                                                                                               cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           >  2:1621752/1‑114 (MQ=255)                                                                                               cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtgct                  >  1:867777/1‑139 (MQ=255)                                                                                                  cAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGcc               <  1:1236753/139‑1 (MQ=255)                                                                                                    gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              <  1:1370788/58‑1 (MQ=255)                                                                                                    gTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              >  2:1370788/1‑58 (MQ=255)                                                                                                         tGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              <  2:1657155/53‑1 (MQ=255)                                                                                                         tGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                              >  1:1657155/1‑53 (MQ=255)                                                                                                          gCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAg       <  1:276733/139‑1 (MQ=255)                                                                                                              ggAGCGGGCTTTCGTAATAATACCCCTACTCTCCCCGACCTTAAACACAA‑CCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCg  <  2:1076876/139‑1 (MQ=255)                                                                                                               gAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                                     <  2:1321152/88‑1 (MQ=255)                                                                                                               gAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                                     >  1:1321152/1‑88 (MQ=255)                                                                                                                aGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTaaa                                                                                                 >  2:1603619/1‑43 (MQ=255)                                                                                                                aGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTaaa                                                                                                 <  1:1603619/43‑1 (MQ=255)                                                                                                                aGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg                    >  2:1257137/1‑120 (MQ=255)                                                                                                                aGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAAtg                    <  1:1257137/120‑1 (MQ=255)                                                                                                                 gCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           >  2:731462/1‑96 (MQ=255)                                                                                                                 gCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                           <  1:731462/96‑1 (MQ=255)                                                                                                                          cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                         <  1:1557954/41‑1 (MQ=255)                                                                                                                          cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                         >  2:1557954/1‑41 (MQ=255)                                                                                                                          cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                      >  2:208038/1‑92 (MQ=255)                                                                                                                          cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                      <  1:208038/92‑1 (MQ=255)                                                                                                                              |                                                                                                                            CACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCG  >  NC_000913/239253‑239501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑