Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,529,938	G→A	pseudogene (2037/2037 nt) R6K (AGA→AAA)	rhsE → ydcD →	pseudogene, Rhs family putative immunity protein for RhsE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,529,938	0	G	A	100.0%	142.6 / NA	46	pseudogene (2037/2037 nt) R6K (AGA→AAA)	rhsE ydcD	pseudogene, Rhs family putative immunity protein for RhsE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/26);  total (20/26)

GCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAG  >  NC_000913/1529805‑1530056                                                                                                                                      |                                                                                                                       gCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   <  2:824954/139‑1 (MQ=255) gCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   <  1:555203/139‑1 (MQ=255)      ttttCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACtt                                                                                                              >  2:1133096/1‑139 (MQ=255)              cAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttt                                                                                                      <  2:536279/139‑1 (MQ=255)                            cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCttt                                                                                        >  1:955881/1‑139 (MQ=255)                                     gaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttg                                                                               <  1:823384/138‑1 (MQ=255)                                     aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                 >  1:693470/1‑137 (MQ=255)                                     aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                 <  2:693470/137‑1 (MQ=255)                                        aaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgttg                                                                            >  1:1217062/1‑139 (MQ=255)                                                 cttggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   <  2:579239/136‑1 (MQ=255)                                                    ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          <  1:1012422/113‑1 (MQ=255)                                                    ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          >  2:1012422/1‑113 (MQ=255)                                                    ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                >  1:476185/1‑139 (MQ=255)                                                          tctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATa                                                          >  1:254688/1‑139 (MQ=255)                                                            ttCGTGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                          >  1:513929/1‑121 (MQ=255)                                                            ttCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                          <  2:513929/121‑1 (MQ=255)                                                              cGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTAGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGTGTTTGATAACaa                                                      >  1:336436/1‑139 (MQ=255)                                                                 gTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTAcc                                                                      >  1:1208119/1‑120 (MQ=255)                                                                 gTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTAcc                                                                      <  2:1208119/120‑1 (MQ=255)                                                                    aGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTAcc                                                                      <  1:94526/117‑1 (MQ=255)                                                                    aGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTAcc                                                                      >  2:94526/1‑117 (MQ=255)                                                                      aTGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAAtt                                              >  1:924474/1‑139 (MQ=255)                                                                         gTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTg                                           <  2:924474/139‑1 (MQ=255)                                                                              aaaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                      <  2:1217062/139‑1 (MQ=255)                                                                                    gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAttt                                >  1:612823/1‑139 (MQ=255)                                                                                       aaTCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTAt                             <  2:254688/139‑1 (MQ=255)                                                                                       aaTCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTAt                             <  2:955881/139‑1 (MQ=255)                                                                                         tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                           <  2:103185/139‑1 (MQ=255)                                                                                         tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                           <  1:426673/139‑1 (MQ=255)                                                                                         tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                           <  1:749885/139‑1 (MQ=255)                                                                                         tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGCTTGATAACAATTCAAATTCt                                            <  1:579938/122‑1 (MQ=255)                                                                                         tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGCTTGATAACAATTCAAATTCt                                            >  2:579938/1‑122 (MQ=255)                                                                                            aaTAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACa                        <  2:476185/139‑1 (MQ=255)                                                                                                 aagcaaagcaAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTa                                                                                                  <  2:254172/60‑1 (MQ=255)                                                                                                 aagcaaagcaAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTa                                                                                                  >  1:254172/1‑60 (MQ=255)                                                                                                   gcaaagcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                <  2:154459/60‑1 (MQ=255)                                                                                                   gcaaagcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                >  1:154459/1‑60 (MQ=255)                                                                                                   gcaaagcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAaca                 >  2:685616/1‑139 (MQ=255)                                                                                                       agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                      >  1:735977/1‑130 (MQ=255)                                                                                                       agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                      <  2:735977/130‑1 (MQ=255)                                                                                                              gAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATAGACATAAAACACCAAAGAGCGt      <  1:1098773/139‑1 (MQ=255)                                                                                                                 ttCAGATGCTTCAAATTATTAAAGGCTAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa            <  1:1194219/130‑1 (MQ=255)                                                                                                                 ttCAGATGCTTCAAATTATTAAAGGCAAACTTTTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                           >  1:724098/1‑115 (MQ=255)                                                                                                                 ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa            >  2:1194219/1‑130 (MQ=255)                                                                                                                 ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTCTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                           <  2:724098/115‑1 (MQ=255)                                                                                                                  tCAGATGCTTCAAATTATTAAAGGTAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTgag  <  2:336436/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                       GCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAG  >  NC_000913/1529805‑1530056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑