Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,529,300	C→T	pseudogene (1399/2037 nt)	rhsE →	pseudogene, Rhs family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,529,300	0	C	T	100.0%	250.9 / NA	73	pseudogene (1399/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (36/37);  total (36/37)

CCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGG  >  NC_000913/1529207‑1529395                                                                                              |                                                                                                ccGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTAGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCAcc                                                                                           <  2:1372518/100‑1 (MQ=255)  cGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTTGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCa                                                                                          <  1:1435513/100‑1 (MQ=255)  cGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCa                                                                                          >  2:300181/1‑100 (MQ=255)      ggCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCg                                                                                      >  1:1786827/1‑100 (MQ=255)      ggCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCg                                                                                      >  2:1735678/1‑100 (MQ=255)         gcTCATCAGCGACGACGGAAATAAGGCGTGGCGCGAGGAGTATGATGAATCGGGCAACCAGCTTAATGAGGGTAACCCGCAGCACTTGCACCGGCCTTAc                                                                                   <  2:1396785/100‑1 (MQ=17)          cTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTAcc                                                                                  <  1:1255285/100‑1 (MQ=255)            catcgGCGACGACAGCAATACGGTGGGGGGCGGGGAGGATGATGACTGGGGCAACCAGCCCACTGAGGAGAACCCGCATCACTTGCACCAGCCGTACCg                                                                                 <  2:961647/99‑1 (MQ=17)            catcaGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTattgc                                                                                >  1:1460074/1‑96 (MQ=255)              tcaGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCt                                                                              >  1:1272410/1‑100 (MQ=255)                 gCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGcc                                                                           <  1:389726/100‑1 (MQ=255)                     aGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAggg                                                                       <  2:1034934/100‑1 (MQ=255)                      gACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgc                                                                      <  1:814556/100‑1 (MQ=255)                      gACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgc                                                                      >  1:315672/1‑100 (MQ=255)                         ggCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAGCCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagc                                                                   <  2:1834037/100‑1 (MQ=255)                         ggCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagc                                                                   >  2:513311/1‑100 (MQ=255)                         ggCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagc                                                                   <  1:337543/100‑1 (MQ=255)                            aaTACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagcagc                                                                >  1:484422/1‑100 (MQ=255)                             aTACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                                                               <  1:541700/100‑1 (MQ=255)                              tACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                                                               >  2:317762/1‑99 (MQ=255)                               aCGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAAGGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatg                                                             <  1:1731758/100‑1 (MQ=255)                                 ggCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATAACTTGCACCAGCCGAACCGTCTGCCAGGGCAGCAGCatg                                                             >  2:1217116/1‑98 (MQ=255)                                  gCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGTACAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatgatg                                                          <  2:1217390/100‑1 (MQ=255)                                   cGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga                                                         <  2:1753558/100‑1 (MQ=255)                                     tGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgagg                                                       <  1:1188018/100‑1 (MQ=255)                                       gcgcGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgaggag                                                     <  2:1950560/100‑1 (MQ=255)                                              gAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGc                                              <  2:1604103/100‑1 (MQ=255)                                              gAGTATGATGAATGGGGCAACCAGCTGGATGGGGAGAAGCCGCATCACTTGCACAAGCCGTAACGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGc                                              <  2:1937207/100‑1 (MQ=17)                                                gTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTg                                            >  2:1441159/1‑100 (MQ=255)                                                 tATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGt                                           <  2:1786812/100‑1 (MQ=255)                                                   tgatgaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAc                                         <  2:1848104/100‑1 (MQ=255)                                                   tgatgaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAc                                         <  1:1327367/100‑1 (MQ=255)                                                    gatgaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACt                                        >  2:829174/1‑100 (MQ=255)                                                    gatgaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACt                                        >  1:1198989/1‑100 (MQ=255)                                                     atgaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACta                                       <  2:750616/100‑1 (MQ=255)                                                       gaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACtata                                     >  1:1349364/1‑100 (MQ=255)                                                       gaATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACtata                                     <  2:660154/100‑1 (MQ=255)                                                           ggggCAACCATCTTAATGAGGATAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCg                                 <  1:884964/100‑1 (MQ=255)                                                            gggCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGt                                >  2:278520/1‑100 (MQ=255)                                                             ggCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTc                               >  1:2005740/1‑100 (MQ=255)                                                              gCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCa                              <  1:953463/100‑1 (MQ=255)                                                               tccgatctttAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCAc                             <  1:295484/92‑1 (MQ=17)                                                                aaCCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCAcc                            <  2:2005722/100‑1 (MQ=255)                                                                   cgatctAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGc                         <  2:938810/95‑1 (MQ=255)                                                                   cAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGc                         >  2:1821673/1‑100 (MQ=255)                                                                    aGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCa                        >  1:616777/1‑100 (MQ=255)                                                                    aGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCa                        >  2:1179797/1‑100 (MQ=255)                                                                      cTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACt                      <  1:1178738/100‑1 (MQ=255)                                                                       ttAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCAcagatcgga                     >  2:295483/1‑92 (MQ=17)                                                                        tAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTAc                    >  1:1712061/1‑100 (MQ=255)                                                                        tAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTAc                    >  2:904691/1‑100 (MQ=255)                                                                        tAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTAc                    >  2:1994882/1‑100 (MQ=255)                                                                         aaTGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCagatcg                   >  1:938814/1‑95 (MQ=255)                                                                          aTGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGa                  >  2:165502/1‑100 (MQ=255)                                                                          aTGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGa                  >  2:165460/1‑100 (MQ=255)                                                                           tGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGAt                 >  1:582921/1‑100 (MQ=255)                                                                            gaggagAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATc                >  2:1444184/1‑100 (MQ=255)                                                                            gaggagAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATc                >  2:244031/1‑100 (MQ=255)                                                                            gaggagAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATc                >  2:1215613/1‑100 (MQ=255)                                                                             aggagAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATcc               >  2:389230/1‑100 (MQ=255)                                                                                  aaCCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGc          <  1:513312/100‑1 (MQ=255)                                                                                   aCCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCa         >  2:1995003/1‑100 (MQ=255)                                                                                   aCCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCa         >  2:1280915/1‑100 (MQ=255)                                                                                    cccGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAg        >  1:282386/1‑100 (MQ=255)                                                                                    cccGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTCTACTATAACCGTCACCGGCACTACGATCCGTTGCAg        <  1:1441168/100‑1 (MQ=255)                                                                                     ccGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgg       >  1:638050/1‑100 (MQ=255)                                                                                     ccGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgg       <  1:456270/100‑1 (MQ=255)                                                                                      cGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAggg      >  1:418763/1‑100 (MQ=255)                                                                                        cATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGc    <  2:1183844/100‑1 (MQ=255)                                                                                        cATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGc    <  2:462767/100‑1 (MQ=255)                                                                                        cATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGc    <  1:1727635/100‑1 (MQ=255)                                                                                          tCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCgg  <  2:315671/100‑1 (MQ=255)                                                                                          tCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCgg  <  2:582919/100‑1 (MQ=255)                                                                                              |                                                                                                CCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGG  >  NC_000913/1529207‑1529395

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑