Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,251,860	(T)7→6	pseudogene (900/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,251,854	0	T	.	100.0%	289.6 / NA	65	pseudogene (894/1323 nt)	yjbI	pseudogene, SopA‑related, pentapeptide repeats‑containing
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (28/37);  total (28/37)

TCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAATTTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCTAT  >  NC_000913/4251720‑4251964                                                                                                                                       |                                                                                                               tCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttt                                                                                                            >  2:159208/1‑139 (MQ=255) tCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttt                                                                                                            >  1:58811/1‑139 (MQ=255)     atgaAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttttatc                                                                                                        >  2:407653/1‑136 (MQ=255)       gaAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCa                                                                                                     <  2:58811/139‑1 (MQ=255)            tAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  2:340392/139‑1 (MQ=255)            tAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  1:69753/139‑1 (MQ=255)             aaCAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTAt                                                                                               >  2:540848/1‑139 (MQ=255)               cAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCg                                                                                             >  2:134380/1‑139 (MQ=255)                 aGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  1:407653/139‑1 (MQ=255)                  gTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATc                                                                                          <  2:543602/139‑1 (MQ=255)                   ttCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCa                                                                                         <  1:159208/139‑1 (MQ=255)                    tCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAg                                                                                        >  2:69987/1‑139 (MQ=255)                     cGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAgg                                                                                       >  1:377333/1‑139 (MQ=255)                      gatgatTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGc                                                                                      >  1:145487/1‑139 (MQ=255)                       atgatTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     >  2:156778/1‑139 (MQ=255)                          atTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  <  1:69987/139‑1 (MQ=255)                               aTGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATc                                                                             <  2:23349/139‑1 (MQ=255)                                    tCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  2:540931/139‑1 (MQ=255)                                      aaCATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           >  2:212499/1‑118 (MQ=255)                                      aaCATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  1:212499/118‑1 (MQ=255)                                             aTTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGatgatatga                                                               >  1:27600/1‑139 (MQ=255)                                              ttCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGatgatatgat                                                              <  2:27600/139‑1 (MQ=255)                                                 aGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCaa                                                           <  1:237208/139‑1 (MQ=255)                                                             ttCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTg                                               >  1:263127/1‑139 (MQ=255)                                                             ttCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTg                                               >  2:20931/1‑139 (MQ=255)                                                              tCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:134380/139‑1 (MQ=255)                                                              tCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:156778/139‑1 (MQ=255)                                                               cGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        >  2:200370/1‑112 (MQ=255)                                                               cGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  1:200370/112‑1 (MQ=255)                                                                gATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  1:501255/139‑1 (MQ=255)                                                                gATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  1:20931/139‑1 (MQ=255)                                                                 aTACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGAt                                                                              >  1:389475/1‑104 (MQ=255)                                                                 aTACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGAt                                                                              <  2:389475/104‑1 (MQ=255)                                                                       aaCAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                >  1:31151/1‑80 (MQ=255)                                                                       aaCAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  2:31151/80‑1 (MQ=255)                                                                         cAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  2:184192/83‑1 (MQ=255)                                                                         cAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           >  1:184192/1‑83 (MQ=255)                                                                          aGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATaaa                                  <  2:27705/139‑1 (MQ=255)                                                                            atgatCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAaga                                >  1:499170/1‑139 (MQ=255)                                                                             tgatCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  1:12867/139‑1 (MQ=255)                                                                               atCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        >  2:121367/1‑96 (MQ=255)                                                                               atCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  1:121367/96‑1 (MQ=255)                                                                                        attaACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGTATCTTTATATAGAGTGGATTCGTAg                    <  1:439632/139‑1 (MQ=255)                                                                                            aCAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGtgat                <  2:145487/139‑1 (MQ=255)                                                                                            aCAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGtgat                <  2:377333/139‑1 (MQ=255)                                                                                              aGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              >  1:80413/1‑107 (MQ=255)                                                                                              aGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  2:80413/107‑1 (MQ=255)                                                                                               gATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTgatgat             >  1:96661/1‑139 (MQ=255)                                                                                                  ttAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  >  1:83134/1‑67 (MQ=255)                                                                                                  ttAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  <  2:83134/67‑1 (MQ=255)                                                                                                       aCGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCAcc     <  2:96661/139‑1 (MQ=255)                                                                                                        cGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:168306/99‑1 (MQ=255)                                                                                                        cGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:168306/1‑99 (MQ=255)                                                                                                          aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:628419/1‑97 (MQ=255)                                                                                                          aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:421889/97‑1 (MQ=255)                                                                                                          aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:421889/1‑97 (MQ=255)                                                                                                          aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:628419/97‑1 (MQ=255)                                                                                                          aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCtat  >  1:162374/1‑139 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     >  1:122123/1‑55 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     <  2:122123/55‑1 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGc                                                        >  2:522801/1‑84 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGc                                                        <  1:522801/84‑1 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               >  1:122059/1‑109 (MQ=255)                                                                                                           aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  2:122059/109‑1 (MQ=255)                                                                                                                           tAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:283656/78‑1 (MQ=255)                                                                                                                           tAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              >  2:283656/1‑78 (MQ=255)                                                                                                                            aaaaaTAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               >  1:333895/1‑92 (MQ=255)                                                                                                                            aaaaaTAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  2:333895/92‑1 (MQ=255)                                                                                                                                       |                                                                                                               TCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAATTTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCTAT  >  NC_000913/4251720‑4251964

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: ‑