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%	173.5 / NA	55	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/29);  total (26/29)

ATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAT  >  NC_000913/239247‑239504                                                                                                                                    |                                                                                                                               aTACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcc                                                                                                                         <  2:1220679/139‑1 (MQ=37)           ttGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTcc                                                                                                               >  1:1410210/1‑139 (MQ=255)             gCTATTAATATTTTGATGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTcccc                                                                                                             >  1:1385602/1‑139 (MQ=255)               catcaaTATTTTGACGCATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGACAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGt                                                                                                           >  1:641066/5‑139 (MQ=255)                 ttAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTcc                                                                                                         <  2:1410210/139‑1 (MQ=255)                   aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                            >  2:346597/1‑134 (MQ=255)                   aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                            <  1:346597/134‑1 (MQ=255)                    atatTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTa                                                                                                      >  2:721783/1‑139 (MQ=255)                        tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAaca                                                                                                  >  2:537822/1‑139 (MQ=255)                           gACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACaa                                                                                               >  2:834042/1‑139 (MQ=255)                            aCGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAc                                                                                              <  1:537822/139‑1 (MQ=255)                              gAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                            <  2:1385602/139‑1 (MQ=255)                               aaTGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAcccc                                                                                           >  2:379324/1‑139 (MQ=255)                                        gTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                  <  2:379578/139‑1 (MQ=255)                                        gTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                  <  1:834042/139‑1 (MQ=255)                                        gTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                  <  1:379324/139‑1 (MQ=255)                                         tATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                 <  2:1086816/139‑1 (MQ=255)                                         tATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                 <  2:496592/139‑1 (MQ=255)                                          aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              >  1:589069/1‑109 (MQ=255)                                          aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                              <  2:589069/109‑1 (MQ=255)                                          aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                 <  1:1005282/122‑1 (MQ=255)                                          aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                 >  2:1005282/1‑122 (MQ=255)                                          aTTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACcaca                                                                                >  1:303825/1‑139 (MQ=255)                                           ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACaa                                                                               >  1:940215/1‑139 (MQ=255)                                             cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAAcc                                                                             >  2:656452/1‑139 (MQ=255)                                                  cAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTaa                                                                                                     >  1:138110/1‑110 (MQ=255)                                                  cAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTaa                                                                                                     <  2:138110/110‑1 (MQ=255)                                                   aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                 >  1:193482/1‑129 (MQ=255)                                                   aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcaccac                                                                                 <  2:193482/129‑1 (MQ=255)                                                     ggTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCa                                                                     >  2:608288/1‑139 (MQ=255)                                                       ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATc                                                                   <  1:656452/139‑1 (MQ=255)                                                          aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcc                                                                                                                         >  1:159706/1‑82 (MQ=255)                                                          aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAcc                                                                                                                         <  2:159706/82‑1 (MQ=255)                                                           gACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                  >  2:1056235/1‑120 (MQ=255)                                                           gACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCa                                                               <  1:1312887/139‑1 (MQ=255)                                                           gACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCCTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                  <  1:1056235/120‑1 (MQ=255)                                                                 aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                            >  1:1289747/1‑88 (MQ=255)                                                                 aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                            <  2:1289747/88‑1 (MQ=255)                                                                   aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTaaa                                                                         <  2:1432516/121‑1 (MQ=255)                                                                   aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTaaa                                                                         >  1:1432516/1‑121 (MQ=255)                                                                     gCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATg                                                     >  2:1126513/1‑139 (MQ=255)                                                                        aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                             >  2:1344029/1‑64 (MQ=18)                                                                        aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                             <  1:1344029/64‑1 (MQ=9)                                                                              agcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                            <  2:641066/139‑1 (MQ=255)                                                                                 cATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                         <  2:940215/139‑1 (MQ=255)                                                                                 cATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACtttt                                         <  2:303825/139‑1 (MQ=255)                                                                                          aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATAtt                                >  1:768323/1‑139 (MQ=255)                                                                                                ccTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCt                                                                            <  1:718214/89‑1 (MQ=255)                                                                                                ccTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCt                                                                            >  2:718214/1‑89 (MQ=255)                                                                                                 cTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCaa                         <  1:608288/139‑1 (MQ=255)                                                                                                    gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                                        <  1:156591/105‑1 (MQ=255)                                                                                                    gCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGcc                                                        >  2:156591/1‑105 (MQ=255)                                                                                                      gTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                              >  1:1362939/1‑113 (MQ=255)                                                                                                      gTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGaaa                                              <  2:1362939/113‑1 (MQ=255)                                                                                                              ttGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGAc            <  2:768323/139‑1 (MQ=255)                                                                                                                  ggggAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCt        <  1:1126513/139‑1 (MQ=255)                                                                                                                        cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAt  >  2:1398712/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                               ATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCAT  >  NC_000913/239247‑239504

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: ‑