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%	223.7 / NA	59	pseudogene (2561/3861 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/32);  total (27/32)

GTTTGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGC  >  NC_000913/1595292‑1595557                                                                                                                                        |                                                                                                                                     gTTTGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCt                                                                                                                                   >  1:649767/1‑139 (MQ=255)        ccTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGtt                                                                                                                            <  2:899615/139‑1 (MQ=255)           tCACCAGTTTAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACg                                                                                                                         <  1:592235/139‑1 (MQ=255)             aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                       <  2:799061/139‑1 (MQ=255)             aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                       <  1:942848/139‑1 (MQ=255)             aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                       <  1:340460/139‑1 (MQ=255)                aGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCtt                                                                                                                    <  2:894937/139‑1 (MQ=255)                aGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCtt                                                                                                                    <  1:642538/139‑1 (MQ=255)                    gAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCa                                                                                                                >  1:585791/1‑139 (MQ=255)                     aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                               <  2:212907/139‑1 (MQ=255)                     aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                               >  2:560340/1‑139 (MQ=255)                        gCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGgtg                                                                                                            >  2:133632/1‑139 (MQ=255)                                      cgtcgtGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGACATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTGGT‑‑CACCCGCGcc                                                                                            >  1:582555/1‑139 (MQ=255)                                                       ttGAGCGTCGTCAGAGGGTTATTCGTCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGa                                                                           <  1:715039/139‑1 (MQ=255)                                                        tGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          <  1:560340/139‑1 (MQ=255)                                                         gAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         <  2:585791/139‑1 (MQ=255)                                                          aGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGc                                                                        >  1:415544/1‑139 (MQ=255)                                                            cgtcgtCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGa                                                                           >  2:183203/1‑134 (MQ=255)                                                            cgtcgtCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGa                                                                           <  1:183203/134‑1 (MQ=255)                                                                          tATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGc                                                                        >  1:28896/1‑123 (MQ=255)                                                                          tATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGc                                                                        <  2:28896/123‑1 (MQ=255)                                                                           aTTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTa                                                                                                                           >  2:67122/1‑73 (MQ=255)                                                                           aTTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTa                                                                                                                           <  1:67122/73‑1 (MQ=255)                                                                                 cATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTc                                                 >  1:234813/1‑139 (MQ=255)                                                                                     ggATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgcag                                             <  2:415544/139‑1 (MQ=255)                                                                                           ttCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         >  1:460561/1‑105 (MQ=255)                                                                                           ttCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         <  2:460561/105‑1 (MQ=255)                                                                                                    ttAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTAt                              <  2:1089552/139‑1 (MQ=255)                                                                                                      aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTa                                                                                                          >  2:1056544/1‑63 (MQ=255)                                                                                                      aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTa                                                                                                          <  1:1056544/63‑1 (MQ=255)                                                                                                      aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCg                            >  2:186637/1‑139 (MQ=255)                                                                                                        gCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGaa                          <  1:667346/139‑1 (MQ=255)                                                                                                           cGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          <  1:476631/88‑1 (MQ=255)                                                                                                           cGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          >  2:476631/1‑88 (MQ=255)                                                                                                            gTCGATAAGCATGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatg                      >  2:209626/1‑139 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTAt                                                                              <  1:772324/82‑1 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTAt                                                                              >  2:772324/1‑82 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          >  1:744537/1‑86 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          <  2:744537/86‑1 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAg                                                     <  1:821069/107‑1 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAg                                                     >  2:821069/1‑107 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAg                                                     >  2:306056/1‑107 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAg                                                     <  1:306056/107‑1 (MQ=255)                                                                                                             tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatga                     >  1:12341/1‑139 (MQ=255)                                                                                                                aTAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATgg                  <  2:649767/139‑1 (MQ=255)                                                                                                                 tAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGt                 <  2:383883/139‑1 (MQ=255)                                                                                                                       cGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCt             <  2:537100/139‑1 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          >  2:1011717/1‑75 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGAc                                                                          <  1:1011717/75‑1 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         >  1:187139/1‑76 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         >  1:341096/1‑76 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         <  2:341096/76‑1 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACg                                                                         <  2:187139/76‑1 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCa          >  2:567930/1‑139 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCa          >  2:130728/1‑139 (MQ=255)                                                                                                                        gTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCa          >  1:1058389/1‑139 (MQ=255)                                                                                                                                tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc  <  2:12341/139‑1 (MQ=255)                                                                                                                                    gtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAAc                                                                                      <  1:178912/51‑1 (MQ=255)                                                                                                                                    gtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAAc                                                                                      >  2:178912/1‑51 (MQ=255)                                                                                                                                        |                                                                                                                                     GTTTGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGT‑‑CACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGC  >  NC_000913/1595292‑1595557

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: ‑