Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_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_pae_pgi	1,529,203	0	C	A	100.0%	68.4 / NA	31	pseudogene (1302/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (19/12);  total (19/12)

CCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCG  >  NC_000913_3_pae_pgi/1529162‑1529347                                          |                                                                                                                                                  ccGGCGCGAAAAGCTCATCTTTATCACGGCGACCACCGGGGACTGCCGCGGGCGCTTACCCCAGCGTTCGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGcc                                       <  1:330404/149‑1 (MQ=11)   ggCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCACC‑CCCTGCACCAGCCGt                                     >  1:948942/1‑149 (MQ=11)    gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTa                                    >  1:1312715/1‑149 (MQ=11)      gcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTAcc                                  <  1:225918/149‑1 (MQ=11)      gcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTAcc                                  <  1:615442/149‑1 (MQ=11)       cgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATCGGGCAACCAGCTTAATGAAGAGAACCCGCATG‑ACCTGCCCCAGCCGtccag                                 >  2:1192086/1‑145 (MQ=11)        gAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGCAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGt                                >  1:1255439/1‑149 (MQ=11)        gAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGt                                >  1:1255451/1‑149 (MQ=11)              ctaatctttATCACCGCGACCACCGGGAACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCGTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCa                          <  2:626703/143‑1 (MQ=14)                 atctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAggg                       <  1:750614/146‑1 (MQ=255)                  tctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGTGCAACCAGCTTAATGAGGAGCACCCGCATC‑ACCTGCACCCGCCGTACCGTCTGCCAGGgc                      >  1:1079001/3‑149 (MQ=11)                    tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGTGCAGCCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGgcag                    >  1:1036062/1‑149 (MQ=14)                    tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGgcag                    >  1:1247305/1‑149 (MQ=255)                         cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCCCCAGCCGTACCGTCTGCCAGGgcagcagca               >  2:1335964/1‑149 (MQ=255)                           cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatg             >  1:454609/1‑149 (MQ=255)                           cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatg             >  1:1281927/1‑149 (MQ=255)                            tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCATGGCGAGGGAAGTATGATGAATGGGGCAACCAGCTTAATGAGGCGAACCCGCATC‑ACCTGCAACAGCCGTACCCTCTCACAGGggcgcagcttca            >  2:85040/1‑145 (MQ=14)                            tGCGACCACCGGGGACAGCCGCTGGCGCTTATCAGCGAAAACGGCAATAACGAGTGGCGCGGGCAGGATGATGGACGGGCACACCAACTTAATGAGGAGAACCCGCATC‑CCGTGCGACAGGATGACCGTTTGTCAGGgcagcctagtgt            >  2:86382/1‑142 (MQ=2)                             gCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGTCAGGGCAGCAGCatgat           <  2:614699/149‑1 (MQ=255)                             gCGACCACCGGGGACTGCCGATGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGATGGGAGTATGATGAATGGGGAAAACAGAATCATGTGGATAACCCGAATC‑ACCTGTACCAGACGGACCGTCTGCCAGGGCAGAAGCatgat           >  1:1033904/1‑149 (MQ=11)                               gACCACCGGGGAGTGCCGGTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga         <  2:793213/149‑1 (MQ=255)                                 ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg                                                                 >  1:805687/1‑92 (MQ=255)                                 ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATgagg                                                                 <  2:805687/92‑1 (MQ=255)                                  caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTACTG‑GCACTACCGCCGGCTTCCAGCGCCAGCCGTACCGTCTGCCAGGGCACCAGCAGGATgaggc      >  2:1004951/1‑148 (MQ=2)                                  caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCa                          <  1:172809/129‑1 (MQ=255)                                  caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCa                          >  2:172809/1‑129 (MQ=255)                                  caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgagga      <  1:267836/149‑1 (MQ=255)                                    ccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt    >  2:403194/1‑149 (MQ=255)                                     cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCa                                                                            <  2:740471/77‑1 (MQ=255)                                     cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCa                                                                            >  1:740471/1‑77 (MQ=255)                                      ggggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCg  <  2:1312715/149‑1 (MQ=255)                                          |                                                                                                                                                  CCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATC‑ACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCG  >  NC_000913_3_pae_pgi/1529162‑1529347

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: ‑