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%	164.8 / 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 (25/29);  total (25/29)

GGCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAA  >  NC_000913/1529804‑1530073                                                                                                                                       |                                                                                                                                        ggCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGc                                                                                                                                     >  1:203658/1‑139 (MQ=255) ggCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGc                                                                                                                                     >  2:342553/1‑139 (MQ=255)                    gTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                                  <  2:376156/139‑1 (MQ=255)                      aGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAGAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAtt                                                                                                                <  2:686836/139‑1 (MQ=255)                        cGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAc                                                                                                              >  1:465859/1‑139 (MQ=255)                         gATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAcc                                                                                                             <  1:438998/139‑1 (MQ=255)                             cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                                  <  1:78947/130‑1 (MQ=255)                             cATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTaa                                                                                                                  >  2:78947/1‑130 (MQ=255)                                    tGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                                  <  1:164359/139‑1 (MQ=255)                                    tGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                                  <  1:81188/139‑1 (MQ=255)                                      aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttg                                                                                                >  1:134887/1‑139 (MQ=255)                                        aaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                                  >  2:506203/1‑135 (MQ=255)                                        aaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAtt                                                                                                  <  1:506203/135‑1 (MQ=255)                                         aaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgttg                                                                                             <  2:261735/139‑1 (MQ=255)                                           tataACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                                           >  2:186649/1‑139 (MQ=255)                                                    gggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                                    >  2:598516/1‑137 (MQ=255)                                                    gggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                                    <  1:598516/137‑1 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                                           <  2:172450/129‑1 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTgttgtt                                                                                           >  1:172450/1‑129 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  1:681986/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  2:565822/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  1:439683/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  2:335977/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  1:576511/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                                 >  1:315090/1‑139 (MQ=255)                                                     ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAAATATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTgtgt                                                                                 >  1:372530/1‑139 (MQ=255)                                                          ctctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGAt                                                                            <  1:186649/139‑1 (MQ=255)                                                           tctTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATa                                                                           <  1:299588/139‑1 (MQ=255)                                                             ttCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAAc                                                                         <  2:134887/139‑1 (MQ=255)                                                                     aGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTCTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCaaa                                                                 >  1:178074/1‑139 (MQ=255)                                                                       aTGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAAtt                                                               >  1:297817/1‑139 (MQ=255)                                                                             taAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACa                                                         <  2:748880/139‑1 (MQ=255)                                                                                aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGCTGCTTCAAATTATTAATGGGAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGCTAACAATTCGAATTCTGACATCg                                                      >  1:528145/1‑139 (MQ=255)                                                                                     gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAttt                                                 >  2:742248/1‑139 (MQ=255)                                                                                     gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAttt                                                 >  1:665842/1‑139 (MQ=255)                                                                                        aaTCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTAt                                              <  2:673416/139‑1 (MQ=255)                                                                                          tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                                            <  1:119837/139‑1 (MQ=255)                                                                                          tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATgg                                            <  2:389973/139‑1 (MQ=255)                                                                                           ccAATAAAAGCAAAGCAAGGTAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTCTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGa                                           <  2:178074/139‑1 (MQ=255)                                                                                               tAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                                       <  2:92702/139‑1 (MQ=255)                                                                                                aaaaGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATaa                                      <  2:465859/139‑1 (MQ=255)                                                                                                          caaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAag                            <  2:359389/139‑1 (MQ=255)                                                                                                             gggAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGc                         >  2:155954/1‑139 (MQ=255)                                                                                                              ggAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCg                        <  2:441063/139‑1 (MQ=255)                                                                                                               gAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGt                       <  2:297817/139‑1 (MQ=255)                                                                                                                aGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGtt                      <  2:137682/139‑1 (MQ=255)                                                                                                                aGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACAAAAAACACCAAAGAGCGtt                      <  1:742248/139‑1 (MQ=255)                                                                                                                  ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTga                    >  1:546802/1‑139 (MQ=255)                                                                                                                   tCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAaca                                  <  2:598737/124‑1 (MQ=255)                                                                                                                   tCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTgag                   <  2:203658/139‑1 (MQ=255)                                                                                                                   tCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCATTTGATTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAaca                                  >  1:598737/1‑124 (MQ=255)                                                                                                                            tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAATACCaaa                             >  2:437398/1‑120 (MQ=255)                                                                                                                            tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCaaa                             <  1:437398/120‑1 (MQ=255)                                                                                                                                    ttaAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGaaaa  <  2:576511/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                        GGCGATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAA  >  NC_000913/1529804‑1530073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑