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%	212.5 / NA	66	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 (33/33);  total (33/33)

ATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTT  >  NC_000913/1529808‑1530065                                                                                                                                   |                                                                                                                                aTTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAAc                                                                                                                         >  2:893344/1‑139 (MQ=255) aTTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAAc                                                                                                                         >  2:532980/1‑139 (MQ=255)                       tGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                                   <  1:162392/139‑1 (MQ=255)                          aTGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                                <  1:532980/139‑1 (MQ=255)                          aTGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                                <  1:893344/139‑1 (MQ=255)                                  aaaaaTATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttg                                                                                        >  1:663997/1‑139 (MQ=255)                                       tataACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTGATTACCCTTTGTTTATTTgttgtt                                                                                   >  2:1583028/1‑139 (MQ=255)                                              cTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTGATTACCCTTTGTTTATTTGTTGTTTACCTTg                                                                            <  1:1583028/139‑1 (MQ=255)                                               tGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAt                                                                                           <  2:955055/123‑1 (MQ=255)                                               tGGGCAACTCTTCGGGTAAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGGTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAt                                                                                           >  1:955055/1‑123 (MQ=255)                                                 ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAtt                                                                                                        <  1:1138594/108‑1 (MQ=255)                                                 ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAtt                                                                                                        >  2:1138594/1‑108 (MQ=255)                                                 ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                         <  2:548313/107‑1 (MQ=255)                                                 ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                         >  1:548313/1‑107 (MQ=255)                                                 ggCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGt                                                                         >  2:1485696/1‑139 (MQ=255)                                                                 aGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCaaa                                                         >  2:643714/1‑139 (MQ=255)                                                                       tataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                                    <  1:1639863/106‑1 (MQ=255)                                                                       tataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                                    >  2:1639863/1‑106 (MQ=255)                                                                        ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                         <  2:1097990/84‑1 (MQ=255)                                                                        ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAt                                                                                                         >  1:1097990/1‑84 (MQ=255)                                                                        ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                                   <  2:517572/90‑1 (MQ=255)                                                                        ataAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                                   >  1:517572/1‑90 (MQ=255)                                                                           aaaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                               <  1:1485696/139‑1 (MQ=255)                                                                           aaaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATc                                               <  1:643714/139‑1 (MQ=255)                                                                            aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                                >  1:830859/1‑89 (MQ=255)                                                                            aaGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTg                                                                                                <  2:830859/89‑1 (MQ=255)                                                                                 gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAAc                                                                                                                         <  1:1485242/59‑1 (MQ=255)                                                                                 gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAAc                                                                                                                         >  2:1485242/1‑59 (MQ=255)                                                                                 gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgttg                                                                                     <  1:611275/95‑1 (MQ=255)                                                                                 gATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATttgttg                                                                                     >  2:611275/1‑95 (MQ=255)                                                                                      tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGt                                                                                                                     <  2:688963/58‑1 (MQ=255)                                                                                      tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGt                                                                                                                     >  1:688963/1‑58 (MQ=255)                                                                                      tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAtt                                                                                                        <  2:1562584/71‑1 (MQ=255)                                                                                      tCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAAtt                                                                                                        >  1:1562584/1‑71 (MQ=255)                                                                                              aagcaaagcaAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACAt                                                <  1:1482955/119‑1 (MQ=255)                                                                                              aagcaaagcaAGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACAt                                                >  2:1482955/1‑119 (MQ=255)                                                                                                gcaaagcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGa                                                   <  1:1449531/114‑1 (MQ=255)                                                                                                gcaaagcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGa                                                   >  2:1449531/1‑114 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAcc                                                                                                     >  2:1395265/1‑60 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTAcc                                                                                                     <  1:1395265/60‑1 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                                    >  2:1161883/1‑77 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTtgttgt                                                                                    <  1:1161883/77‑1 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                               <  1:818315/130‑1 (MQ=255)                                                                                                    agcaaGGGAGTTCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                               >  2:818315/1‑130 (MQ=255)                                                                                                           aggTTCATTTGCTGCAAATTTTTAAAGTAAATCTTGTCATTTTGTTAATTACCGTTTGTGTATTTGTGGTTTACCTTGGGTTTGATAACAATTAAAATTCTCACATCGTTTTTTATAGACACAAAACACCAAAGAGCGt               <  1:416421/137‑1 (MQ=255)                                                                                                              ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAt                                                                                           <  2:971198/60‑1 (MQ=255)                                                                                                              ttCAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTAt                                                                                           >  1:971198/1‑60 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttttt                                                                                                             >  2:24844/1‑40 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCAtttttt                                                                                                             <  1:24844/40‑1 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                                   <  2:1077999/50‑1 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCt                                                                                                   >  1:1077999/1‑50 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATaaa                             <  2:877128/120‑1 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATaaa                             >  1:877128/1‑120 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGt               >  2:1448057/1‑134 (MQ=255)                                                                                                                cAGATGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGt               <  1:1448057/134‑1 (MQ=255)                                                                                                                   aTGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACa                                                 <  2:448081/97‑1 (MQ=255)                                                                                                                   aTGCTTCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACa                                                 >  1:448081/1‑97 (MQ=255)                                                                                                                       ttCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCg                <  1:1096392/126‑1 (MQ=255)                                                                                                                       ttCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCg                >  2:1096392/1‑126 (MQ=255)                                                                                                                        tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAtttt                                        >  2:794289/1‑101 (MQ=255)                                                                                                                        tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAtttt                                        <  1:794289/101‑1 (MQ=255)                                                                                                                        tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAtttt                                        <  1:1156139/101‑1 (MQ=255)                                                                                                                        tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTAtttt                                        >  2:1156139/1‑101 (MQ=255)                                                                                                                        tCAAATTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCGTGTGTTTGTTAACAATTCAAATTCTTACATCGTTTTTTATGGACATAAAACACCTAAGAGCGGTGAGCTAGATcct  >  2:416421/1‑137 (MQ=255)                                                                                                                           aaTTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATa                               >  2:965834/1‑107 (MQ=255)                                                                                                                           aaTTATTAAAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTAGGTTTGATAACAATTGAAATTCTGACATCGTATTTTATGGACATa                               <  1:965834/107‑1 (MQ=255)                                                                                                                                   |                                                                                                                                ATTTTTCTGCCAAATGTAGCGATGCATGTATTGAAAAATATAACACTGGGCAACTCTTCGGGTTAGATGGTATAAAAGCAGATAATCCAATAAAAGCAAAGCAAGGGAGTTCAGATGCTTCAAATTATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTT  >  NC_000913/1529808‑1530065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑