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%	175.9 / NA	54	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 (26/28);  total (26/28)

TCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAG  >  NC_000913/1529813‑1530056                                                                                                                              |                                                                                                                       tCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTc                                                                                                           >  1:1034591/1‑139 (MQ=255)           gTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                 <  2:439343/139‑1 (MQ=255)                   gCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCtt                                                                                         <  1:1307759/139‑1 (MQ=255)                    cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          >  2:1566957/1‑137 (MQ=255)                    cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          <  1:1566957/137‑1 (MQ=255)                             aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   >  2:43407/1‑103 (MQ=255)                             aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   <  1:43407/103‑1 (MQ=255)                             aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttg                                                                               >  1:787706/1‑139 (MQ=255)                                  tataACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                          <  2:787706/139‑1 (MQ=255)                                         cTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAATCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   <  2:1034591/139‑1 (MQ=255)                                          tGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   >  2:982285/1‑138 (MQ=255)                                          tGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   <  1:982285/138‑1 (MQ=255)                                            ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                >  1:1443011/1‑139 (MQ=255)                                                 ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   >  1:286568/1‑83 (MQ=255)                                                 ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   <  2:286568/83‑1 (MQ=255)                                                 ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCtt                                                                                         <  2:735670/109‑1 (MQ=255)                                                 ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCtt                                                                                         >  1:735670/1‑109 (MQ=255)                                                    ttCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                 >  2:168689/1‑98 (MQ=255)                                                    ttCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                 <  1:168689/98‑1 (MQ=255)                                                      cGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGAt                                                           <  2:862495/134‑1 (MQ=255)                                                      cGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGAt                                                           >  1:862495/1‑134 (MQ=255)                                                              aTGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   <  2:867747/70‑1 (MQ=255)                                                              aTGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCa                                                                                                                   >  1:867747/1‑70 (MQ=255)                                                                   ataAAAGCAGATCATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttt                                                                                                      <  2:1153817/78‑1 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttt                                                                                                      >  1:1153817/1‑78 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCtt                                                                                         >  2:1674265/1‑91 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCtt                                                                                         <  1:1674265/91‑1 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgt                                                                              >  2:236753/1‑102 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgt                                                                              <  1:236753/102‑1 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAAtt                                              <  1:157747/134‑1 (MQ=255)                                                                   ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAAtt                                              >  2:157747/1‑134 (MQ=255)                                                                        aGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGt                                    <  2:1443011/139‑1 (MQ=255)                                                                            gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          <  1:948292/81‑1 (MQ=255)                                                                            gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                          >  2:948292/1‑81 (MQ=255)                                                                            gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                 >  2:328836/1‑90 (MQ=255)                                                                            gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                 <  1:328836/90‑1 (MQ=255)                                                                            gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAttt                                >  1:1109559/1‑139 (MQ=255)                                                                                   cAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAAtt                                                    <  1:616939/112‑1 (MQ=255)                                                                                   cAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAAtt                                                    >  2:616939/1‑112 (MQ=255)                                                                                     aTAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTAt                             <  1:35236/133‑1 (MQ=255)                                                                                     aTAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTAt                             >  2:35236/1‑133 (MQ=255)                                                                                       aaaaGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAgg                                                                                                                     >  2:1150416/1‑43 (MQ=255)                                                                                       aaaaGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAgg                                                                                                                     <  1:1150416/43‑1 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTAcc                                                                      <  2:674492/72‑1 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   >  1:1265393/1‑75 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                   <  2:1265393/75‑1 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGt                                    >  2:364773/1‑106 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGt                                    <  1:364773/106‑1 (MQ=255)                                                                                                         ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGCTTATTTGTTGTTTAcc                                                                      >  1:674492/1‑72 (MQ=255)                                                                                                          tCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTgag  <  2:1109559/139‑1 (MQ=255)                                                                                                           cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGAt                                                           <  2:670350/81‑1 (MQ=255)                                                                                                           cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGAt                                                           >  1:670350/1‑81 (MQ=255)                                                                                                              aTGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                       <  1:927226/50‑1 (MQ=255)                                                                                                              aTGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                       >  2:927226/1‑50 (MQ=255)                                                                                                                              |                                                                                                                       TCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAG  >  NC_000913/1529813‑1530056

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: ‑