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%	67.9 / NA	30	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (11/19);  total (11/19)

GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACC  >  NC_000913_3_pae_pgi/1529153‑1529363                                                                  |                                                                                                                                                   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)                                  cccTGCGACCAACGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                               <  1:306721/147‑1 (MQ=255)                                       cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCTTGACCGTCTGCCAGGGCAGCAGCatgatg                          <  2:1016013/149‑1 (MQ=14)                                       cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatgatg                          <  1:879505/149‑1 (MQ=255)                                       cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCCCATCACCTGCACCAGCTGTACCGTCTGCCAGGGCAGCAGCatgatg                          >  1:373706/1‑149 (MQ=255)                                        gACCACGGGGGGCTGCCGCTGGCGAGTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTGAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga                         <  1:959653/149‑1 (MQ=14)                                        gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga                         <  1:196936/149‑1 (MQ=255)                                         agcaccGGGGACTGCGGCTGGGGCTTAGCAGCGAAGACGGCAATACGGGGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAAGGAGGAGAACCCGCAGCAACTGCACCAGCCGTACCGCCTGCCAGGGCAGCAGCATGATgag                        <  2:73880/147‑1 (MQ=14)                                         accacgGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGGGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag                        <  1:107704/149‑1 (MQ=255)                                         accaccGGGGACCGCCGCTGGCGTTTACCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag                        <  2:795326/149‑1 (MQ=14)                                              cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTg                                             >  1:370044/1‑123 (MQ=255)                                              cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTg                                             <  2:370044/123‑1 (MQ=255)                                              cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                                       >  1:396586/1‑129 (MQ=255)                                              cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                                       <  2:396586/129‑1 (MQ=255)                                                   acTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGc              <  2:184637/148‑1 (MQ=255)                                                     tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTCCCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTg            >  2:1017557/1‑149 (MQ=255)                                                               gcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAcc  <  1:22592/149‑1 (MQ=255)                                                               gcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAcc  >  1:375989/1‑149 (MQ=255)                                                                  |                                                                                                                                                   GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTAT‑GATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACC  >  NC_000913_3_pae_pgi/1529153‑1529363

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: ‑