Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_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_hsa_pgi	1,529,203	0	C	A	100.0%	136.9 / NA	50	pseudogene (1302/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (21/29);  total (21/29)

TACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCA  >  NC_000913_3_hsa_pgi/1529183‑1529298                     |                                                                                                tatcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCtt                      <  2:4703598/93‑1 (MQ=11) tatcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTa                     <  2:3665706/94‑1 (MQ=11) tatcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTa                     <  1:773411/94‑1 (MQ=11) tatcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTa                     <  1:4205353/94‑1 (MQ=11) tatcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAAt                   >  1:4526069/4‑99 (MQ=11)  atcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATg                  <  1:1830474/97‑1 (MQ=11)  atcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATg                  <  2:1845862/97‑1 (MQ=11)  atcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATg                  <  2:5334066/97‑1 (MQ=255)   tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTatg                                          >  2:842478/2‑74 (MQ=11)   tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                >  1:2173415/2‑100 (MQ=255)   tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATga                 <  2:346601/98‑1 (MQ=255)   tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATga                 <  1:1990842/98‑1 (MQ=255)   tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCCCCGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                >  2:316439/2‑100 (MQ=11)    cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGCAGACGGCAATACGGCGCGGCGCGGGGCGTATGATGAATGGGGCAACCAGCTTACTgag                >  2:5077819/1‑99 (MQ=11)    cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTatga                                         <  1:843185/74‑1 (MQ=11)    cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGCGGCGCGGGGAGTATGATGAATGGGGCAACCAGCt                       >  2:3481525/1‑92 (MQ=11)    cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAAAACGGCGTGGCGCGGGGAGTCTGATGAAAGCGGCAACCAGCTTaa                    >  2:706509/1‑95 (MQ=11)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGTCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagga              <  1:2284537/100‑1 (MQ=11)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagga              <  2:5215948/100‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagga              <  1:2526224/100‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagga              <  1:1380210/100‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagga              <  2:2752434/100‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg               <  1:4814082/99‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg               <  1:5511007/99‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg               <  2:5520421/99‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg               <  1:2604405/99‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg               <  1:1611357/99‑1 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                >  1:3025936/1‑98 (MQ=255)     aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                >  2:5422815/1‑98 (MQ=255)      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAGTGGGGCAACCAGCTTAATgag                >  2:314745/1‑97 (MQ=11)      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCCACCAGCTTAATgag                >  2:5324593/1‑97 (MQ=11)      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgaggag             <  2:2684071/100‑1 (MQ=255)      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgaggag             <  2:2683664/100‑1 (MQ=255)      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgag                >  2:2136281/1‑97 (MQ=12)       tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgaggag             >  1:2335199/1‑99 (MQ=255)        gCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAAGGGGGCAACCAGCTTAATgag                >  2:5944070/1‑95 (MQ=11)        gCGACCACCGGGGACTGCCGCCGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAGGGGGGCAACCAGCTTAATgag                >  2:5943976/1‑95 (MQ=11)         cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAc          >  2:3265639/1‑100 (MQ=255)          gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAcc         >  1:4947856/1‑100 (MQ=255)          gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAcc         <  1:278857/100‑1 (MQ=255)           accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAccc        <  2:2045285/100‑1 (MQ=255)           accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAccc        >  1:4956288/1‑100 (MQ=255)           accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAccc        >  1:2795339/1‑100 (MQ=255)            ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAccc        <  2:4483772/99‑1 (MQ=255)              accGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGATGAGAACCCg       >  2:3853910/1‑98 (MQ=255)               ccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCAt    <  2:5045066/100‑1 (MQ=255)                cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCAt    >  1:2737926/1‑99 (MQ=255)                 ggggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCa     <  2:212228/97‑1 (MQ=255)                 ggggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCa  <  2:4495873/100‑1 (MQ=255)                 ggggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCa  <  1:1517455/100‑1 (MQ=255)                     |                                                                                                TACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCA  >  NC_000913_3_hsa_pgi/1529183‑1529298

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑