Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,428,079	C→T	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA → ytfB ←	pseudogene, related to transcriptional regulators OapA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,428,079	0	C	T	100.0%	207.8 / NA	65	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA ytfB	pseudogene, related to transcriptional regulators OapA family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/34);  total (31/34)

ATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTTT  >  NC_000913/4427948‑4428208                                                                                                                                    |                                                                                                                                  atatTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACcgcg                                                                                                                            <  1:899447/139‑1 (MQ=255)               aCCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTg                                                                                                              >  2:1531426/1‑139 (MQ=255)               aCCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTg                                                                                                              >  2:355114/1‑139 (MQ=255)                         gCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCt                                                                                                    <  2:1721843/139‑1 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           >  1:1310614/1‑111 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           <  2:1310614/111‑1 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               >  2:319477/1‑139 (MQ=255)                               gcTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCggg                                                                                              >  1:1375053/2‑139 (MQ=255)                                      tATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                       <  1:413519/139‑1 (MQ=255)                                      tATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                       <  2:1571499/139‑1 (MQ=255)                                        tCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGa                                                                                     <  2:1261533/139‑1 (MQ=255)                                        tCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGa                                                                                     <  1:1531426/139‑1 (MQ=255)                                        tCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACACTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGa                                                                                     <  1:1160521/139‑1 (MQ=255)                                           caTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                  <  1:1653866/139‑1 (MQ=255)                                            aTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTg                                                                                 <  1:1137972/139‑1 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                  >  2:1505066/1‑137 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                  <  1:1505066/137‑1 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                >  1:1354596/1‑139 (MQ=255)                                              cAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGtt                                                                               <  2:1375053/139‑1 (MQ=255)                                                 tATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGat                                                                            >  1:975812/1‑139 (MQ=255)                                                       ttCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcc                                                                      <  2:1354596/139‑1 (MQ=255)                                                         cACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcccc                                                                    >  1:402669/1‑139 (MQ=255)                                                           ccccAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           >  1:1259393/1‑82 (MQ=255)                                                           ccccAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           <  2:1259393/82‑1 (MQ=255)                                                           ccccAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCAc                                                                                                                         >  2:1480875/1‑84 (MQ=255)                                                           ccccAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCAc                                                                                                                         <  1:1480875/84‑1 (MQ=255)                                                           ccccAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGt                                                                  >  1:57430/1‑139 (MQ=255)                                                               acgCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTGTGGTTGACCCTTCATTTACCGCGCACGAATAAATCTGCCATCCGGCGGGCGGGTGAACAGGACCGGTTGATTATTCCCCGTATCa                                                              <  1:1057054/137‑1 (MQ=255)                                                               aGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              <  1:355114/139‑1 (MQ=255)                                                                ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCaa                                                             >  2:907759/1‑139 (MQ=255)                                                                     tGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                       >  2:1156467/1‑108 (MQ=255)                                                                     tGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                       <  1:1156467/108‑1 (MQ=255)                                                                          gCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGcc                                                   >  2:163797/1‑139 (MQ=255)                                                                             aGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGt                                                <  2:57430/139‑1 (MQ=255)                                                                               aCGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTca                                              >  1:1587205/1‑139 (MQ=255)                                                                                   aaGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           <  1:1087719/58‑1 (MQ=255)                                                                                   aaGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           >  2:1087719/1‑58 (MQ=255)                                                                                    aGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    <  2:509770/96‑1 (MQ=255)                                                                                    aGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    >  1:509770/1‑96 (MQ=255)                                                                                     ggTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              <  1:83993/117‑1 (MQ=255)                                                                                     ggTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              >  2:83993/1‑117 (MQ=255)                                                                                        catcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCAcgccgc                                     >  2:1780159/1‑139 (MQ=255)                                                                                         atcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              <  1:544051/113‑1 (MQ=255)                                                                                         atcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              >  2:544051/1‑113 (MQ=255)                                                                                          tcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               >  2:837100/1‑79 (MQ=255)                                                                                          tcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               <  1:837100/79‑1 (MQ=255)                                                                                          tcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTg                                   >  2:1307406/1‑139 (MQ=255)                                                                                                agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTcacca                                           >  2:1142521/1‑125 (MQ=255)                                                                                                agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTcacca                                           <  1:1142521/125‑1 (MQ=255)                                                                                                   cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTAt                                                                <  1:710724/101‑1 (MQ=255)                                                                                                   cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTAt                                                                >  2:710724/1‑101 (MQ=255)                                                                                                   cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTgg                          >  2:1308881/1‑139 (MQ=255)                                                                                                   cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTgg                          <  1:1505627/139‑1 (MQ=255)                                                                                                   cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTgg                          <  2:402669/139‑1 (MQ=255)                                                                                                    aaTCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                  >  2:1552948/1‑82 (MQ=255)                                                                                                    aaTCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                  <  1:1552948/82‑1 (MQ=255)                                                                                                      tCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAg                                                     <  1:1530574/109‑1 (MQ=255)                                                                                                      tCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAg                                                     >  2:1530574/1‑109 (MQ=255)                                                                                                       ccTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGa                      <  1:783203/139‑1 (MQ=255)                                                                                                                  ttttGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcc                                                                      >  2:882671/1‑80 (MQ=255)                                                                                                                  ttttGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcc                                                                      <  1:882671/80‑1 (MQ=255)                                                                                                                     tGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAgg                                                                                      >  2:596893/1‑61 (MQ=255)                                                                                                                     tGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAgg                                                                                      <  1:596893/61‑1 (MQ=255)                                                                                                                          gACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGtt   <  1:1780159/139‑1 (MQ=255)                                                                                                                           aCCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGttt  >  2:699609/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                  ATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTTT  >  NC_000913/4427948‑4428208

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: ‑