Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,544,384	C→T	pseudogene (381/381 nt)	yddK ←	pseudogene, leucine‑rich protein, putative glycoportein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,544,384	0	C	T	100.0%	195.0 / NA	60	pseudogene (381/381 nt)	yddK	pseudogene, leucine‑rich protein, putative glycoportein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/30);  total (30/30)

TAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTT  >  NC_000913/1544252‑1544506                                                                                                                                     |                                                                                                                           tAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTaaaaa                                                                                                                      >  2:114713/1‑139 (MQ=255)   aCCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAgg                                                                                                                    >  1:615915/1‑139 (MQ=255)               ggTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTgga                                                                                                        >  2:400772/1‑139 (MQ=255)                    aTCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGaaa                                                                                                   >  1:105325/1‑139 (MQ=255)                         tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                <  2:901991/137‑1 (MQ=255)                         tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:615915/139‑1 (MQ=255)                         tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  1:934439/139‑1 (MQ=255)                         tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTAATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                >  1:901991/1‑137 (MQ=255)                          gAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                             <  1:114713/139‑1 (MQ=255)                                aTGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCa                                                                                       >  2:355702/1‑139 (MQ=255)                                              cccTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGt                                                                         <  2:152134/139‑1 (MQ=255)                                                 ttCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                       <  1:246830/138‑1 (MQ=255)                                                 ttCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                       >  2:246830/1‑138 (MQ=255)                                                  tCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     <  1:355702/139‑1 (MQ=255)                                                         gTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                             >  2:617458/1‑108 (MQ=255)                                                         gTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                             <  1:617458/108‑1 (MQ=255)                                                            aaTCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                           <  2:878513/139‑1 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAAc                                                                                                            >  1:291047/1‑77 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAAc                                                                                                            <  2:291047/77‑1 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  1:1245123/91‑1 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              >  2:1245123/1‑91 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                       >  1:1555682/1‑114 (MQ=255)                                                                         aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                       <  2:1555682/114‑1 (MQ=255)                                                                               tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                        <  1:400772/139‑1 (MQ=255)                                                                                 aCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGt                                                                                 <  1:979597/96‑1 (MQ=255)                                                                                 aCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGt                                                                                 >  2:979597/1‑96 (MQ=255)                                                                                 aCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTGTCTTATTGCCTGATTGtaat                                                <  2:993892/129‑1 (MQ=255)                                                                                 aCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaat                                                >  1:993892/1‑129 (MQ=255)                                                                                 aCTATATTATCAACAAGACC‑‑ACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:56508/81‑1 (MQ=255)                                                                                 aCTATATTATCAACAAGACC‑‑ACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              >  1:56508/1‑81 (MQ=255)                                                                                            aacaaGACCATACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                <  2:1331591/70‑1 (MQ=255)                                                                                            aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                >  1:1331591/1‑70 (MQ=255)                                                                                             acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCgg                                                                          >  1:1416139/1‑91 (MQ=255)                                                                                             acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCgg                                                                          <  2:1416139/91‑1 (MQ=255)                                                                                                 gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGttt                      >  1:1630585/1‑139 (MQ=255)                                                                                                           ttATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:1484291/57‑1 (MQ=255)                                                                                                           ttATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              >  1:1484291/1‑57 (MQ=255)                                                                                                           ttATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTa            <  2:105325/139‑1 (MQ=255)                                                                                                             ataGAATTATTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     <  1:1277545/80‑1 (MQ=255)                                                                                                             ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     >  2:1277545/1‑80 (MQ=255)                                                                                                                   ttAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                           <  1:73110/84‑1 (MQ=255)                                                                                                                   ttAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                           >  2:73110/1‑84 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGt                                                                         <  2:684146/68‑1 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGt                                                                         >  1:684146/1‑68 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     >  2:682289/1‑72 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     <  1:682289/72‑1 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGcc                                                          <  2:1506807/83‑1 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGcc                                                          >  1:1506807/1‑83 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagta                            <  1:1456677/113‑1 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagta                            >  2:1456677/1‑113 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagt                                 >  1:279703/1‑108 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagt                                 <  2:279703/108‑1 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt  >  2:1224512/1‑139 (MQ=255)                                                                                                                     aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt  >  2:1620874/1‑139 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             <  1:537183/90‑1 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             >  2:537183/1‑90 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             <  1:303389/90‑1 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             >  2:303389/1‑90 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttat                                       <  2:37519/96‑1 (MQ=255)                                                                                                                           gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttat                                       >  1:37519/1‑96 (MQ=255)                                                                                                                                     |                                                                                                                           TAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTT  >  NC_000913/1544252‑1544506

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: ‑