Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	1,529,185	C→T	pseudogene (1284/2037 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	1,529,185	0	C	T	100.0%	15.0 / NA	13	pseudogene (1284/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (6/7);  total (6/7)

GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGC  >  NC_000913_3_pae_pgi/1529153‑1529330                                 |                                                                                                                                                   gAATACAAACCGGGGCGGAAAGCTCTTTTGTATCACTGCGTACACCGTGGACTGCCGCTGGTGCTTATGAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGTAGAACCCGCATCACCt                               <  2:69382/149‑1 (MQ=11)       acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCa                         >  1:995405/1‑149 (MQ=1)                   aaaGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCt             >  2:196936/1‑149 (MQ=11)                       ctCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCa         >  1:474273/2‑149 (MQ=11)                        ccATCTTTATCGCTGCGACCACCGGGGACTGCCGCGGGGGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAg        <  1:199063/148‑1 (MQ=14)                        ccATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAg        <  1:428578/148‑1 (MQ=255)                          atctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTg                              <  1:154258/122‑1 (MQ=255)                          atctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTg                              >  2:154258/4‑125 (MQ=11)                           tctttATCACTGGGACCACCGGGGACTGCCGCTGGCGCTTAGCAGCGAAGACGGCAATACGGCGGGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgc     <  2:294532/147‑1 (MQ=14)                             tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcag   <  2:776860/149‑1 (MQ=255)                              ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTCTGGAATCATTTTG‑AACCAGCTTAATGCGGTGGACCCGCATCACCTGCACCCGACCTAGCGTCTGCCAGGgcagc  <  2:1010643/149‑1 (MQ=9)                              ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGGCAGggcggc  >  1:90120/1‑149 (MQ=11)                              ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCCGGgccgc  >  2:966093/1‑149 (MQ=14)                                 |                                                                                                                                                   GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGC  >  NC_000913_3_pae_pgi/1529153‑1529330

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: ‑