Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_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_vch_pgi	1,529,218	0	C	T	100.0%	11.9 / NA	7	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (4/3);  total (4/3)

ATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACC  >  NC_000913_3_vch_pgi/1529178‑1529363                                         |                                                                                                                                                  atctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                                       >  1:112717/4‑149 (MQ=255)           cggCGACCACCGGGGACTGCCGGTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatg                             <  2:90202/147‑1 (MQ=255)           cTGCGACCACCGGGGACTGCCGCTGGCGCTTCTCAGCGAAGACGGCAATACGGCGGGGCGCGGGGAGTATGATGAAGGGGGCAACCAGCTTCATGAAGAGAACCCGCATCACCTGCACCAGCCAGACCGTTAGCCAGGgccgcagcaag                             >  2:4459/1‑147 (MQ=14)              caaccacaGGCGACCGCCGCAGGCGCATACCAGCGAAAACGGCAATACGGCCTGGCGCCGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAAAACTCGCATCACCTGCACCAGACGTACCGTCTGCCAGGGCAGCAGCatgatg                          <  1:299237/147‑1 (MQ=14)                              ccGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTa          <  2:205719/149‑1 (MQ=255)                                gCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGCACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGGCGGGGCGGTACt        >  1:56061/1‑149 (MQ=255)                                      gcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAcc  >  1:273567/1‑149 (MQ=255)                                         |                                                                                                                                                  ATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACC  >  NC_000913_3_vch_pgi/1529178‑1529363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑