Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_bme_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_bme_pgi	1,529,203	0	C	A	100.0%	30.2 / NA	17	pseudogene (1302/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (8/9);  total (8/9)

ACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGG  >  NC_000913_3_bme_pgi/1529161‑1529348                                           |                                                                                                                                                  acCGGCGGGAAAAGCTCATCTTTAGCACGGCGACCACCGGGGACTGCCGCGGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGCGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGc                                         <  2:325000/149‑1 (MQ=11)       gcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAcc                                   >  1:709198/1‑149 (MQ=11)          aaaaGCTCATCTTTATCACTGCGACCACCTGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTc                                <  1:717679/149‑1 (MQ=11)             agctCATCTTTAGCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGc                             <  2:61822/146‑1 (MQ=14)                     tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACAGCAATACGGCGGGGCGCGGGGAGTATGATGAATGGGGCAACCCGCTTAATGAGGAGAACCCGCATCACCCGCACCAGCCGTACCGTCTGCCAGGgcag                     >  2:138715/1‑149 (MQ=14)                      ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                    >  1:48886/1‑149 (MQ=255)                         tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGGGGAGAACCCGCATCACCTGCACCCACCGTACCGTCTGCCAGGgcagcagc                 >  2:328751/2‑149 (MQ=14)                         tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagc                 <  1:53894/148‑1 (MQ=255)                         tcACGGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagc                 <  1:460673/148‑1 (MQ=255)                           aCTGCGACCACCGGGGACTGCCGCTGGCGCTAATCATCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCat               >  1:202670/1‑149 (MQ=255)                            cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGCGGCGCGGGGAGTATGCTGAAACCGGCAACCAGCTCAATGAGGAGAACCCGCATCACCACCACCAACCGCACCGCCTGCCAGGccagcacgatg              >  2:724602/1‑144 (MQ=14)                              gCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatgat            <  1:562026/149‑1 (MQ=255)                                gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTCCCGTCTGCAAGGGGAGCAGCAtgctga          >  2:188716/1‑149 (MQ=14)                                 accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACTTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag         <  2:358662/149‑1 (MQ=255)                                   caccGGGGAGTGCGGCTGGCGCTTAGCAGCGAAGACGGCAATACGGCGGGGCGCGGGAAGTATAATCAATGGGGCAACCAGCTTAACGAGGAGAACCCGTATCTCCTGCACCAGCCGTATCGTCTGCCAGGGTATCAGCATGATgagga       <  2:754585/149‑1 (MQ=14)                                     ccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGAAAAAGCCATACCGTATGCCAGGGCAGCAGCATGATgaggaga     >  2:376016/1‑148 (MQ=11)                                        gggACTGCGGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgg  <  2:824073/149‑1 (MQ=255)                                           |                                                                                                                                                  ACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGG  >  NC_000913_3_bme_pgi/1529161‑1529348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑