Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,068,276	Δ1 bp	intergenic (+22/+235)	ymdF → / ← rutG	KGG family protein/pyrimidine permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,276	0	G	.	100.0%	257.9 / NA	63	intergenic (+22/+235)	ymdF/rutG	KGG family protein/pyrimidine permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (26/37);  total (26/37)

TGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068155‑1068410                                                                                                                          |                                                                                                                                       tGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCg                                                                                                                     >  2:825887/1‑139 (MQ=255)  ggACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGt                                                                                                                    >  2:1148725/1‑139 (MQ=255)   gACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                                                   <  1:204805/124‑1 (MQ=255)   gACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                                                   >  2:204805/1‑124 (MQ=255)   gACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTc                                                                                                                   <  1:166238/139‑1 (MQ=255)        cacagcGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCaaaaa                                                                                                              >  1:653880/1‑139 (MQ=255)                gggTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAc                                                                                                      <  1:168480/139‑1 (MQ=255)                gggTAATTTCAAGAATGACCCACAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAc                                                                                                      <  1:874568/139‑1 (MQ=255)                  gTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccg                                                                                                    >  2:1477396/1‑139 (MQ=255)                   tAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccgc                                                                                                   <  1:1148725/139‑1 (MQ=255)                           aGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                                           <  2:309212/139‑1 (MQ=255)                             aaTGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:825887/139‑1 (MQ=255)                             aaTGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:788053/139‑1 (MQ=255)                             aaTGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:460451/139‑1 (MQ=255)                                 aCCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggtgg                                                                                     >  2:686542/1‑139 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  2:100811/1‑125 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:100811/125‑1 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtga                                                                           >  2:1525061/1‑139 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtga                                                                           >  1:339623/1‑139 (MQ=255)                                              aTCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtgatga                                                                        <  1:1571515/139‑1 (MQ=255)                                                        ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGCAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCAGCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              >  1:1048544/1‑139 (MQ=255)                                                        ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              <  2:1371975/139‑1 (MQ=255)                                                        ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              <  1:588513/139‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                                           <  2:784850/108‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                                           >  1:784850/1‑108 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCt                                                            <  1:677166/139‑1 (MQ=255)                                                                  gtggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:1395506/102‑1 (MQ=255)                                                                  gtggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  1:1395506/1‑102 (MQ=255)                                                                   tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATg                                                   >  1:620586/1‑139 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgc                                                  >  1:1339327/1‑139 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgc                                                  >  2:809606/1‑139 (MQ=255)                                                                     gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  1:1477396/139‑1 (MQ=255)                                                                     gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:516186/139‑1 (MQ=255)                                                                     gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:1608906/139‑1 (MQ=255)                                                                     gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:998157/139‑1 (MQ=255)                                                                       aaGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               <  2:620586/139‑1 (MQ=255)                                                                          agCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            <  1:1263948/139‑1 (MQ=255)                                                                            cAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGTTTACCCg                                                                                         >  1:416580/1‑92 (MQ=255)                                                                            cAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:416580/92‑1 (MQ=255)                                                                              gTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccgc                                                                                                   <  1:1274182/80‑1 (MQ=255)                                                                              gTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccgc                                                                                                   >  2:1274182/1‑80 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  1:1019280/1‑89 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:1019280/89‑1 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTAt                                       >  1:107773/1‑139 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTAt                                       >  2:960012/1‑139 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTAt                                       <  2:107773/139‑1 (MQ=255)                                                                                   ggCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAgg                                   <  1:809606/139‑1 (MQ=255)                                                                                     cAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGcc                                 <  1:306284/139‑1 (MQ=255)                                                                                        aaGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGa                                              <  1:785468/123‑1 (MQ=255)                                                                                        aaGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGa                                              >  2:785468/1‑123 (MQ=255)                                                                                         aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  2:1324831/1‑79 (MQ=255)                                                                                         aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:1324831/79‑1 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            >  2:1547186/2‑113 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            <  1:1547186/112‑1 (MQ=255)                                                                                                        ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               >  1:668677/1‑106 (MQ=255)                                                                                                        ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               <  2:668677/106‑1 (MQ=255)                                                                                                         gCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  1:1427057/1‑63 (MQ=255)                                                                                                         gCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:1427057/63‑1 (MQ=255)                                                                                                          cTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAatatat            <  1:1525061/139‑1 (MQ=255)                                                                                                          cTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAatatat            <  2:843661/139‑1 (MQ=255)                                                                                                            aaTCGATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggt                                                                                       <  1:1269763/62‑1 (MQ=255)                                                                                                            aaTCGATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggt                                                                                       >  2:1269763/1‑62 (MQ=255)                                                                                                                    aCGAAT‑CATTTTT‑TCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGTCTACCAGAAGATTGCAATATATTGAATTTGCa  <  1:686542/139‑1 (MQ=255)                                                                                                                          |                                                                                                                                       TGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068155‑1068410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑