Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,528,418	C→A	pseudogene (529/2049 nt)	rhsE →	RhsE protein in rhs element

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,528,418	0	C	A	100.0%	47.4 / NA	20	pseudogene (529/2049 nt)	rhsE	RhsE protein in rhs element
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (12/8);  total (12/8)

CAGCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCC  >  NC_000913/1528283‑1528461                                                                                                                                        |                                            cAGCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGc                                         >  2:874026/1‑140 (MQ=25)   gCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCAc                                       <  2:916655/140‑1 (MQ=21)   gCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCAc                                       <  2:315525/140‑1 (MQ=21)   gCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCAc                                       <  1:906084/140‑1 (MQ=21)          aaCAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCt                                >  2:461425/1‑140 (MQ=21)               ccTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACa                           >  1:563727/1‑140 (MQ=21)               ccTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACa                           >  2:218547/1‑140 (MQ=21)               ccTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGCGTGCGCACCATCGCACCAGACCTGGACa                           >  2:564847/1‑140 (MQ=21)                cTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACAt                          <  1:471354/140‑1 (MQ=21)                cTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACAt                          <  1:338914/140‑1 (MQ=21)                 tGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATc                         >  1:82267/1‑140 (MQ=37)                 tGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATc                         >  1:565998/1‑140 (MQ=37)                    tgtATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGc                      <  2:864251/140‑1 (MQ=18)                     gtATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCa                     <  2:446551/140‑1 (MQ=18)                         gACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATccc                 >  2:195319/1‑140 (MQ=18)                         gACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGGGTGCGCACCATCGCACCAGACCTGGACATCCGCATccc                 >  2:269657/1‑140 (MQ=17)                              tGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATCCCGTATg            >  2:23462/1‑140 (MQ=17)                              tGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATCCCGTATg            >  1:625698/1‑140 (MQ=18)                              tGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATCCCGTATg            >  2:651676/1‑140 (MQ=18)                              tGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATCCCGTATg            >  1:506802/1‑140 (MQ=18)                                        tGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCATCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGAccc  <  2:625698/140‑1 (MQ=17)                                                                                                                                        |                                            CAGCACCTGAACAGCCTGGTGTATGACCGTGACTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCC  >  NC_000913/1528283‑1528461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑