Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,595,427	A→G	pseudogene (2561/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,595,427	0	A	G	100.0%	180.2 / NA	49	pseudogene (2561/3861 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/24);  total (25/24)

CTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTC  >  NC_000913/1595300‑1595562                                                                                                                                |                                                                                                                                        cTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTa                                                                                                                              <  2:828880/139‑1 (MQ=255)  ttCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTAc                                                                                                                             >  1:364352/1‑139 (MQ=255)          ttGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTc                                                                                                                     <  2:93037/139‑1 (MQ=255)              aCGCCGACATGACTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAgg                                                                                                                 >  1:753897/1‑139 (MQ=255)                    aCATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGa                                                                                                                                    >  1:699377/1‑114 (MQ=255)                    aCATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTCATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGTCCGTCCCGTTTGCCTGa                                                                                                                                    <  2:699377/114‑1 (MQ=255)                              cgtcgtGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGcc                                                                                                 >  2:303840/1‑139 (MQ=255)                                   tgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCcaacaa                                                                                            >  2:737461/1‑139 (MQ=255)                                   tgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACaa                                                                                            >  1:575476/1‑139 (MQ=255)                                       ccAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTAAGGCACGTCGATAAGCACGTCGCCCGTCCAGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAg                                                                                        >  1:737277/1‑139 (MQ=255)                                               ttGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGa                                                                                <  2:364352/139‑1 (MQ=255)                                                tGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGAc                                                                               <  2:321790/139‑1 (MQ=255)                                                tGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGAc                                                                               <  2:345345/139‑1 (MQ=255)                                                 gAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACg                                                                              <  2:53146/139‑1 (MQ=255)                                                  aGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGc                                                                             <  1:826865/139‑1 (MQ=255)                                                       cgtcAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGata                                                                        >  2:376187/1‑139 (MQ=255)                                                       cctcAGAGGGTTATTCGCCATGGGATCATTCCACGGTCTAGGCACGTAGATAAGCACGTCGCCCGTCCTGTTTGCCTGATAGTTAGGGCCTTTCCAGCTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGata                                                                        >  1:241498/3‑139 (MQ=255)                                                          cAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGatatat                                                                     <  1:376187/139‑1 (MQ=255)                                                               ggTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTcc                                                                                                                    <  1:55028/87‑1 (MQ=255)                                                               ggTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTcc                                                                                                                    >  2:55028/1‑87 (MQ=255)                                                                   aTTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCcgcg                                                            >  1:352668/1‑139 (MQ=255)                                                                    ttCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACg                                                                              >  1:816066/1‑120 (MQ=255)                                                                    ttCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACg                                                                              <  2:816066/120‑1 (MQ=255)                                                                         cATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCATGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTc                                                      >  1:685568/1‑139 (MQ=255)                                                                         cATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTc                                                      >  2:493439/1‑139 (MQ=255)                                                                             ggATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgcag                                                  <  1:616737/139‑1 (MQ=255)                                                                              gATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgcagc                                                 <  2:123532/139‑1 (MQ=255)                                                                              gATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgcagc                                                 <  1:486192/139‑1 (MQ=255)                                                                                        cGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGa                                                                                                                                    >  1:876684/1‑46 (MQ=255)                                                                                        cGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGa                                                                                                                                    <  2:876684/46‑1 (MQ=255)                                                                                           tttAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTa                                    >  2:446486/1‑139 (MQ=255)                                                                                            gtAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCAACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGAAGCAGGAATATCCGTAt                                   >  2:689059/2‑139 (MQ=255)                                                                                              aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGa                                                                                                                                    >  1:378328/1‑40 (MQ=255)                                                                                              aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGa                                                                                                                                    <  2:378328/40‑1 (MQ=255)                                                                                              aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCg                                 >  2:329046/1‑139 (MQ=255)                                                                                                    gTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTa                                                                                    >  2:1100838/1‑82 (MQ=255)                                                                                                    gTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTa                                                                                    <  1:1100838/82‑1 (MQ=255)                                                                                                     tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGgt                                                                                                                <  1:505239/53‑1 (MQ=255)                                                                                                     tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGgt                                                                                                                >  2:505239/1‑53 (MQ=255)                                                                                                        aTAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATgg                       <  1:59571/139‑1 (MQ=255)                                                                                                         tAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGt                      <  2:82756/139‑1 (MQ=255)                                                                                                          aaGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCttt                                                                                                                      <  1:453530/42‑1 (MQ=255)                                                                                                          aaGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCttt                                                                                                                      >  2:453530/1‑42 (MQ=255)                                                                                                                gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGTAGGAATATCCGTATCGAAAATGATGGTACCTCCa               >  1:949442/1‑139 (MQ=255)                                                                                                                 tCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatgat                         >  2:310221/1‑128 (MQ=255)                                                                                                                 tCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatgat                         <  1:310221/128‑1 (MQ=255)                                                                                                                 tCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCAt              >  1:986811/1‑139 (MQ=255)                                                                                                                         cccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGcc      <  1:868489/139‑1 (MQ=255)                                                                                                                             tttGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTc  <  2:493735/139‑1 (MQ=255)                                                                                                                                |                                                                                                                                        CTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTC  >  NC_000913/1595300‑1595562

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑