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%	12.6 / NA	8	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (5/3);  total (5/3)

CGGAATACACACCGGCGCGAAAAG‑TTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTA  >  NC_000913_3_pae_pgi/1529151‑1529358                                                                     |                                                                                                                                             cGGAATACACACCGGCGCGAAAAGCTACACTTTCA‑CACGGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAAACGGCAATACGGCGTGGCGCGGGGAGTCTGATGAATGGGGCCACCAGCTTAATGAGGAGAACCCGCATccc                                                             >  2:194272/1‑147 (MQ=11)                 gcgAAAAG‑CTCATCTTTATCACTGCGCCCAACGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAcc                                             <  1:72798/149‑1 (MQ=14)                 gcgAAAAG‑CTCATCTTTATCACTGCGACCACCGGGGACTGCCGATCGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAcc                                             <  1:159394/149‑1 (MQ=11)                          ctCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGACCCAGACGTACCGTCTGCCa                                     >  1:92198/2‑149 (MQ=11)                                                      acTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggg          >  1:106786/2‑148 (MQ=255)                                                      acTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggg          <  2:106786/147‑1 (MQ=255)                                                        tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCAGGGGGAATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGATGAGTCTGGGATg       >  2:210692/1‑149 (MQ=14)                                                             cTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACta  >  1:13510/1‑149 (MQ=255)                                                                     |                                                                                                                                             CGGAATACACACCGGCGCGAAAAG‑TTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTA  >  NC_000913_3_pae_pgi/1529151‑1529358

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑