Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,529,350	Δ1 bp	pseudogene (1461/2049 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	1,529,347	0	G	.	100.0%	84.2 / NA	24	pseudogene (1458/2049 nt)	rhsE	RhsE protein in rhs element
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (13/11);  total (13/11)

TCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGAATCCCATACAAGTGATAG  >  NC_000913/1529217‑1529474                                                                                                                                   |                                                                                                                                tcatcaGCGGAGACGTCAATACGGCGAGGCGCTGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg                                                                                                                               <  2:226406/133‑1 (MQ=255) tcatcaGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg                                                                                                                               <  1:99143/133‑1 (MQ=255)    tcaGCGAAGATGGCACTACGGCGTAGGGTGGGAAGTATGATTAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCCCCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggctg                                                                                                                            <  2:179883/133‑4 (MQ=17)             aCGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAAc                                                                                                                  >  2:273611/1‑133 (MQ=255)                   aTACGGCGTGGCGCGAGGCGTAAGATGAATCGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCAc                                                                                                            <  1:164297/133‑1 (MQ=17)                           tGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTa                                                                                                    >  1:509130/1‑133 (MQ=255)                                           atgaATGGGGCACCCAGCTTAAGGAGGAGACCCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgggg                                                                                    <  2:310954/133‑1 (MQ=14)                                           atgaATGGGGCAACCAGTTTAATGAGGAGACCCCGCATCACCGGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgggg                                                                                    <  2:509130/133‑1 (MQ=14)                                                   ggCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTatat                                                                            >  2:36917/1‑133 (MQ=255)                                                        ccAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCAccc                                                                       >  2:379747/1‑133 (MQ=255)                                                              tAATGAGGAGAACCCGCATCCCCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGAcc                                                                 <  2:270176/133‑1 (MQ=255)                                                                   aggagAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGAtt                                                            <  1:379747/133‑1 (MQ=255)                                                                      agaACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTggg                                                         >  1:382804/1‑133 (MQ=255)                                                                      agaACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTggg                                                         >  1:77214/1‑133 (MQ=255)                                                                         aCCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTg                                                      >  1:27096/1‑133 (MQ=255)                                                                          cccGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTga                                                     >  2:388557/1‑133 (MQ=255)                                                                          cccGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTga                                                     >  2:74256/1‑133 (MQ=255)                                                                            cGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTgaga                                                   <  1:273611/133‑1 (MQ=255)                                                                              cATCACCTGCGCCAGTCGTACCATCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAgg                                                 <  1:245808/133‑1 (MQ=18)                                                                                    cTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGCCGGTATATTACCGCGGTCCCGCTTGAGTTGAGAGGtggatg                                           >  2:183031/1‑133 (MQ=17)                                                                                                  ccGTCTGCTAGGGCAACAACATTATGAGGATTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGt                             <  1:183031/133‑1 (MQ=18)                                                                                                    gTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTAt                           >  2:303067/1‑133 (MQ=255)                                                                                                    gTCTGCCAGGGCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTAt                           >  1:472636/1‑133 (MQ=255)                                                                                                            gggCAGCAGCATGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGaa                   <  2:19741/133‑1 (MQ=255)                                                                                                                agcagcaTGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGAATccc               <  1:74256/133‑1 (MQ=255)                                                                                                                 gcagcaTGATGAGGAGTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGAATCCCa              <  1:36917/133‑1 (MQ=255)                                                                                                                            aggagTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCGGTTGAAACCCATAAAAGTGATa   >  1:247229/1‑133 (MQ=21)                                                                                                                             ggagTC‑GGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGAATCCCATACAAGTGATAg  <  2:77214/133‑1 (MQ=255)                                                                                                                                   |                                                                                                                                TCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATATGTATCAGTATCCGTTGAATCCCATACAAGTGATAG  >  NC_000913/1529217‑1529474

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑