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%	178.7 / NA	55	pseudogene (381/381 nt)	yddK	pseudogene, leucine‑rich protein, putative glycoportein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/28);  total (27/28)

CTAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAAC  >  NC_000913/1544251‑1544512                                                                                                                                      |                                                                                                                                 cTAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTaaaa                                                                                                                             <  1:824283/139‑1 (MQ=255) cTAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTaaaa                                                                                                                             <  1:1043454/139‑1 (MQ=255)            aCGGGTTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAAc                                                                                                                  <  2:1435941/139‑1 (MQ=255)                          tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                    <  2:1411504/139‑1 (MQ=255)                                tATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTcc                                                                                              >  2:636951/1‑139 (MQ=255)                                     cATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAg                                                                                         <  1:636951/139‑1 (MQ=255)                                      aTGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACGCTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCTGAAgg                                                                                        >  1:935684/1‑139 (MQ=255)                                                   tCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                                   <  2:15359/115‑1 (MQ=255)                                                   tCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                                   >  1:15359/1‑115 (MQ=255)                                                           tGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGcc                                                                                                                        >  1:1224706/1‑86 (MQ=255)                                                           tGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGcc                                                                                                                        <  2:1224706/86‑1 (MQ=255)                                                            gAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTg                                                                  <  1:160197/139‑1 (MQ=255)                                                                         tACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaata                                                     >  1:1017126/1‑139 (MQ=255)                                                                           cATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                                   <  2:935684/139‑1 (MQ=255)                                                                                tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGaa                                                                                                                   <  1:1153986/70‑1 (MQ=255)                                                                                tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGaa                                                                                                                   >  2:1153986/1‑70 (MQ=255)                                                                                tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                                   <  1:1346194/134‑1 (MQ=255)                                                                                tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                                   >  2:1346194/1‑134 (MQ=255)                                                                                tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                              >  2:1190876/1‑139 (MQ=255)                                                                                  aCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttatt                                            <  2:1017126/139‑1 (MQ=255)                                                                                      tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGTGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                             <  1:773291/102‑1 (MQ=255)                                                                                      tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGTGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                             >  2:773291/1‑102 (MQ=255)                                                                                      tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                    <  1:702678/79‑1 (MQ=255)                                                                                      tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                    >  2:702678/1‑79 (MQ=255)                                                                                              acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTAtt                                >  2:1292459/1‑139 (MQ=255)                                                                                                     cAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAt                          >  1:337317/1‑138 (MQ=255)                                                                                                     cAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAt                          <  2:337317/138‑1 (MQ=255)                                                                                                       gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAg                                                                                         >  2:1259069/1‑73 (MQ=255)                                                                                                       gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAg                                                                                         <  1:1259069/73‑1 (MQ=255)                                                                                                       gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                                 <  2:286162/97‑1 (MQ=255)                                                                                                       gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                                 >  1:286162/1‑97 (MQ=255)                                                                                                        acacTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAg                                                                                         >  2:1219272/1‑72 (MQ=255)                                                                                                        acacTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAg                                                                                         <  1:1219272/72‑1 (MQ=255)                                                                                                              ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                           >  1:778109/1‑80 (MQ=255)                                                                                                              ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                           <  2:778109/80‑1 (MQ=255)                                                                                                                  aaTTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGa                                                             >  2:687096/1‑90 (MQ=255)                                                                                                                  aaTTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGa                                                             <  1:687096/90‑1 (MQ=255)                                                                                                                    ttAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagt                                       >  2:1005880/1‑110 (MQ=255)                                                                                                                    ttAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagt                                       <  1:1005880/110‑1 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaata                                                     >  2:667964/1‑94 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaata                                                     <  1:667964/94‑1 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATc                                                  >  1:603659/1‑97 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATc                                                  <  2:603659/97‑1 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                              >  1:761162/1‑101 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                              <  2:761162/101‑1 (MQ=255)                                                                                                                      aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt        >  2:514413/1‑139 (MQ=255)                                                                                                                        tgatgaTTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                              <  1:151046/99‑1 (MQ=255)                                                                                                                        tgatgaTTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                              >  2:151046/1‑99 (MQ=255)                                                                                                                          atgatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttatt                                            >  2:936633/1‑99 (MQ=255)                                                                                                                          atgatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtt                                               >  2:1130257/1‑96 (MQ=255)                                                                                                                          atgatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtt                                               <  1:1130257/96‑1 (MQ=255)                                                                                                                          atgatTTATTCATTAAAAAGGCCATGAACTCGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttatt                                            <  1:936633/99‑1 (MQ=255)                                                                                                                            gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAtt                         <  1:1162332/116‑1 (MQ=255)                                                                                                                            gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAtt                         >  2:1162332/1‑116 (MQ=255)                                                                                                                            gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAAc  >  2:372/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                 CTAACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAAC  >  NC_000913/1544251‑1544512

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: ‑