Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	1,529,218	C→T	pseudogene (1317/2037 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	1,529,218	0	C	T	100.0%	146.6 / NA	50	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/24);  total (26/24)

ACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAC  >  NC_000913_3_pae_pgi/1529157‑1529362                                                              |                                                                                                                                                  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                                           <  1:359644/135‑1 (MQ=255)                               aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGc                                           >  2:359644/1‑135 (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                       <  4:76196/150‑1 (MQ=255)                                    gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag                       >  2:580325/1‑150 (MQ=255)                                       caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                                                                                >  2:228283/1‑90 (MQ=255)                                       caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                                                                                <  1:228283/90‑1 (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)                                                 tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAc                                                                          >  3:82863/1‑86 (MQ=255)                                                 tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAc                                                                          <  4:82863/86‑1 (MQ=255)                                                  gCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTa         <  1:1057494/150‑1 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGCTGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGACGAGGAGTCGGGGCTGTAc        >  4:372050/1‑150 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCa                                                            >  2:1065358/1‑98 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCa                                                            <  1:1065358/98‑1 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCAc                                                           >  1:235113/1‑99 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCAc                                                           <  2:235113/99‑1 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcag                                   >  4:337412/1‑123 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcag                                   <  3:337412/123‑1 (MQ=255)                                                   ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAc        >  4:192586/1‑150 (MQ=255)                                                    cGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACt       <  1:551987/150‑1 (MQ=255)                                                     gCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACta      <  1:580325/150‑1 (MQ=255)                                                      cTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACtat     >  1:765674/1‑150 (MQ=255)                                                      cTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACtat     <  4:693841/150‑1 (MQ=255)                                                      cTGGCGCTTATCAACGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTaa                                                                                    <  2:1064253/71‑1 (MQ=14)                                                      cTGGCGCTTATCAACGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTaa                                                                                    >  1:1064253/1‑71 (MQ=14)                                                        ggCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATaa   <  4:316936/150‑1 (MQ=255)                                                        ggCGCTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATaa   <  1:39836/150‑1 (MQ=255)                                                         gcgcTTATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAc  >  1:720887/1‑150 (MQ=255)                                                         gcgcTTATCAGCGAAGACGGCAATACGCCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAc  >  1:818187/1‑150 (MQ=255)                                                              |                                                                                                                                                  ACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGG‑CGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAC  >  NC_000913_3_pae_pgi/1529157‑1529362

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: ‑