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%	145.3 / NA	47	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 (20/27);  total (20/27)

CAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCG  >  NC_000913/1529818‑1530051                                                                                                                         |                                                                                                                  cAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttt                                                                                                 <  2:1326240/139‑1 (MQ=255)     tGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTa                                                                                             <  1:1217531/139‑1 (MQ=255)       tAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                           <  2:872165/139‑1 (MQ=255)             atcATGTATTGAAAAATATAACACTGCGCAACTCTTCGAGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAGGCAAGGGAGTTCAGGTGCTTCAAATTATTAAAGGCAGACTTGTCATTTTTTTAATTACCCt                                                                                     <  2:152103/137‑1 (MQ=255)               cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtt                                                                                                   <  2:334544/123‑1 (MQ=255)               cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtt                                                                                                   >  1:334544/1‑123 (MQ=255)                 tGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGTAAGGGAGTTCAGATGCTACAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                           >  2:921353/1‑129 (MQ=255)                 tGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                           <  1:921353/129‑1 (MQ=255)                 tGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCATTTGt                                                                                 >  2:762798/1‑139 (MQ=255)                           aaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                     <  1:1115908/125‑1 (MQ=255)                           aaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                     >  2:1115908/1‑125 (MQ=255)                                    cTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                              <  2:1028148/139‑1 (MQ=255)                                     tGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                      >  2:937558/1‑130 (MQ=255)                                     tGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                      <  1:937558/130‑1 (MQ=255)                                     tGGGCAAATCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTgg                                                             >  2:937540/1‑139 (MQ=255)                                       ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTa                                                                                             >  1:621744/1‑105 (MQ=255)                                       ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTa                                                                                             <  2:621744/105‑1 (MQ=255)                                       ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                              >  1:27809/1‑136 (MQ=255)                                       ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                              <  2:27809/136‑1 (MQ=255)                                            ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAcc                                                                                       >  1:1431925/1‑106 (MQ=255)                                            ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAcc                                                                                       <  2:1431925/106‑1 (MQ=255)                                                               taAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACa                                   <  2:1030111/139‑1 (MQ=255)                                                                 aaaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                 <  1:937540/139‑1 (MQ=255)                                                                  aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCt                                       <  1:1295707/132‑1 (MQ=255)                                                                  aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCt                                       >  2:1295707/1‑132 (MQ=255)                                                                  aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                 >  2:712634/1‑138 (MQ=255)                                                                  aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                 <  1:712634/138‑1 (MQ=255)                                                                            tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTg                                      >  2:196974/1‑123 (MQ=255)                                                                            tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTg                                      <  1:196974/123‑1 (MQ=255)                                                                                aTAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAATAATTCAAATTCTGACATCGTATTTTATGGACAt                  >  1:343781/1‑139 (MQ=255)                                                                                 tAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                     >  1:35400/1‑87 (MQ=255)                                                                                 tAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                     <  2:35400/87‑1 (MQ=255)                                                                                 tAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                      <  1:222720/134‑1 (MQ=255)                                                                                 tAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                      >  2:222720/1‑134 (MQ=255)                                                                                   aaagcaaagcAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATaaa               <  1:838680/139‑1 (MQ=255)                                                                                          agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTTTTGTTTACCTTGGGTTTGATAACAAtt                                               <  2:853858/100‑1 (MQ=255)                                                                                          agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                              >  2:655551/1‑85 (MQ=255)                                                                                          agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                              <  1:655551/85‑1 (MQ=255)                                                                                          agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGTTAACAAtt                                               >  1:853858/1‑100 (MQ=255)                                                                                           gcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAATAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa       <  2:343781/139‑1 (MQ=255)                                                                                           gcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACa                   >  2:769088/1‑127 (MQ=255)                                                                                           gcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACa                   <  1:769088/127‑1 (MQ=255)                                                                                               gggAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa       >  2:552505/1‑135 (MQ=255)                                                                                               gggAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa       <  1:552505/135‑1 (MQ=255)                                                                                                ggAGTTCAGATGCTTATAATTATTAAAGGCAAACTTGTCATTTTTTTATTTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAATTTCTGACATCGTATTTTACGGACATAAAACACCAAAGAGCg  <  1:762798/139‑1 (MQ=255)                                                                                                    ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCt                                                                <  2:498120/73‑1 (MQ=255)                                                                                                    ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCt                                                                >  1:498120/1‑73 (MQ=255)                                                                                                                         |                                                                                                                  CAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCG  >  NC_000913/1529818‑1530051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑