Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	1,529,203	C→A	pseudogene (1302/2037 nt)	rhsE →	pseudogene, Rhs family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	1,529,203	0	C	A	100.0%	73.5 / NA	28	pseudogene (1302/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (15/13);  total (15/13)

ACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGG  >  NC_000913_3_pae_pgi/1529157‑1529349                                               |                                                                                                                                                    acacacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCAcc                                             >  3:316936/1‑150 (MQ=1)   acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAg                                           >  2:551987/1‑150 (MQ=11)      ccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCg                                        >  4:79341/1‑150 (MQ=11)        ggCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTa                                      <  3:193970/150‑1 (MQ=11)        ggCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAAGACGGCGCGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGACGAGAAACCGAATCACCGGCACCAGCCGTa                                      >  2:468093/1‑150 (MQ=11)         gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAc                                     <  1:1123212/150‑1 (MQ=11)         gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAc                                     <  1:243124/150‑1 (MQ=11)                     cATCTTTATCACTGTGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGAGGAAGGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                         <  2:230581/150‑1 (MQ=11)                     cATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                         <  4:61658/150‑1 (MQ=255)                         tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGGATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCCGACCGTCTGCCAGGgcagc                     >  4:151838/1‑150 (MQ=11)                          ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGCGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagca                    >  3:341458/1‑150 (MQ=255)                             tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                 <  4:61043/149‑1 (MQ=255)                               aCTGCGCCCACCGGGGACTGCCGCTGGCGCTTATCAGCGACGACGCCACTACGGCGTGG‑CGCGCGGAGTATGATGAATCGGGCAACCCGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCAGACCCGTATGGCAGCgcggcagcaag               >  2:850850/1‑148 (MQ=11)                               aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGc                              >  2:359644/1‑135 (MQ=255)                               aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGc                              <  1:359644/135‑1 (MQ=255)                                cTGCGACCACCGGTGACTTCCCGTGGCCCTTATCAGCGAAGTCGGTAGAAC‑GTGTGGTCGCTGGGATTATTAGGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatga              <  1:850850/150‑1 (MQ=9)                                cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGGGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatga              >  2:379234/1‑150 (MQ=255)                                 tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatgat             <  1:675172/150‑1 (MQ=255)                                   cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga           <  2:124649/150‑1 (MQ=255)                                    gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGACCCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag          >  1:674225/1‑150 (MQ=255)                                    gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag          >  2:580325/1‑150 (MQ=255)                                    gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag          <  4:76196/150‑1 (MQ=255)                                       caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                                                                   <  1:228283/90‑1 (MQ=255)                                       caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                                                                   >  2:228283/1‑90 (MQ=255)                                        accGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt      >  3:693841/1‑150 (MQ=255)                                        accGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAAGACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCAGCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt      <  1:797185/150‑1 (MQ=255)                                          cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCg    >  3:3455/1‑150 (MQ=255)                                          cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCg    >  2:8107/1‑150 (MQ=255)                                            ggggCTGGCGGTGGCGCTTATCAGCGAAGGCGGCAATAGGGCGTGG‑CGTGGGGCGTGTGATGAGTGGGGCAAACAGCGTAATGAGGAGAAGCCGCATCACCTGCACCAGCCGTACCGCCTGCCAGGGCAGCAGCGTGATGAGGAGTCggg  >  4:441528/1‑150 (MQ=18)                                               |                                                                                                                                                    ACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGG  >  NC_000913_3_pae_pgi/1529157‑1529349

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑