Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,068,456	A→G	intergenic (+202/+55)	ymdF → / ← rutG	conserved protein YmdF/pyrimidine:H(+) symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,456	0	A	G	100.0%	156.7 / NA	47	intergenic (+202/+55)	ymdF/rutG	conserved protein YmdF/pyrimidine:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (31/16);  total (31/16)

TGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAACAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCATTGAGTAAAA  >  NC_000913/1068325‑1068584                                                                                                                                    |                                                                                                                                 tggtTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGt                                                                                                                          <  1:1231586/140‑1 (MQ=255) tggtTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGt                                                                                                                          <  1:550498/140‑1 (MQ=255)    ttGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACg                                                                                                                       <  1:463027/140‑1 (MQ=255)     tGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGt                                                                                                                      <  1:460209/140‑1 (MQ=255)      gATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGt                                                                                                                      <  1:747828/139‑1 (MQ=255)      gATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGt                                                                                                                      >  2:747828/1‑139 (MQ=255)             atgaCAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTcaaca                                                                                                              >  1:996566/1‑140 (MQ=255)             atgaCAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTcaaca                                                                                                              >  1:684728/1‑140 (MQ=255)                aCAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTca                                                                                                                 <  2:373509/134‑1 (MQ=255)                aCAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTca                                                                                                                 >  1:373509/1‑134 (MQ=255)                  aaaTGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGt                                                                                                                      <  1:1041818/127‑1 (MQ=255)                  aaaTGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGt                                                                                                                      >  2:1041818/1‑127 (MQ=255)                  aaaTGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTg                                                                                                         >  2:1134948/1‑140 (MQ=255)                                   aTGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCAcc                                                                                                     >  1:1357483/1‑127 (MQ=255)                                   aTGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGAATGAGCAATGCGTACGTTGTCAACAATCTGCAcc                                                                                                     <  2:1357483/127‑1 (MQ=255)                                    ggcgcGATGCTTATCAGGCTTACCAGAAGATTGAAATATATTAAATTTGCATTTTTTTGTAGGCCGGATAAGGTGTTTACGCCGCATCCGGCAGGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCcgg                                                                                       <  2:366714/139‑1 (MQ=25)                                              ttATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTg                                                                             <  1:1056156/140‑1 (MQ=255)                                               tATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGt                                                                            >  1:1015641/1‑140 (MQ=255)                                                     gCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATgg                                                                      >  2:1327367/1‑140 (MQ=255)                                                     gCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATgg                                                                      >  2:980248/1‑140 (MQ=255)                                                         aCCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTcc                                                                  >  1:1472074/1‑140 (MQ=255)                                                                gattaaaaTATTTTGATTTTGCTTTTTTTTGAGGGCCGGAAAGGGCTTTACCGCCGCACCCGGCAGGAGAAATGCGTATTTTTTCAACATTCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGaa                                                           <  2:391692/134‑1 (MQ=255)                                                                gaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGaa                                                           >  1:391692/1‑140 (MQ=255)                                                                   tGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGaacaa                                                        >  2:19013/1‑140 (MQ=255)                                                                               aaTTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCACCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTg                                            >  2:1103645/1‑140 (MQ=255)                                                                                     cACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGt                                      >  2:13516/1‑140 (MQ=255)                                                                                      aCTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCACCTGATGAACAACtt                                                     <  1:1311428/124‑1 (MQ=255)                                                                                      aCTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCACCTGATGAACAACtt                                                     >  2:1311428/1‑124 (MQ=255)                                                                                        tGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTcaa                                   <  2:996566/140‑1 (MQ=255)                                                                                              gTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACt                             <  1:970006/140‑1 (MQ=255)                                                                                              gTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACt                             <  1:1327367/140‑1 (MQ=255)                                                                                                aGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCACCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACttt                           <  1:1103645/140‑1 (MQ=255)                                                                                                  gCCGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCt                         >  1:917618/1‑140 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACttt                           <  1:1195292/136‑1 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACttt                           >  2:1195292/1‑136 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGc                       >  1:612127/1‑140 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGc                       >  1:48220/1‑140 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGc                       >  1:1457463/1‑140 (MQ=255)                                                                                                    cGGATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGc                       >  2:1389253/1‑140 (MQ=255)                                                                                                     ggATAAGGTTTTTCCGCGGCATCGGGCAGGAGCAATGCGTACTTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      <  1:746919/140‑1 (MQ=255)                                                                                                     ggATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      <  1:1389253/140‑1 (MQ=255)                                                                                                      gATAAGGCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCtt                     >  2:33944/1‑140 (MQ=255)                                                                                                            gCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      <  2:1495053/133‑1 (MQ=255)                                                                                                            gCGTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      >  1:1495053/1‑133 (MQ=255)                                                                                                              gTTTACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGc             >  2:818021/1‑140 (MQ=255)                                                                                                               tttACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCa            <  2:1457463/140‑1 (MQ=255)                                                                                                                ttACGCCGCATCCGGCATGAGTAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCAt           >  2:1086402/1‑140 (MQ=255)                                                                                                                ttACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      >  2:1514294/1‑129 (MQ=255)                                                                                                                ttACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCt                      <  1:1514294/129‑1 (MQ=255)                                                                                                                ttACGCCGCATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCAt           <  2:1015641/140‑1 (MQ=255)                                                                                                                      cgcATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCa            <  2:974522/133‑1 (MQ=255)                                                                                                                      cgcATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCa            >  1:974522/1‑133 (MQ=255)                                                                                                                       gcATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCa            >  2:1116928/1‑132 (MQ=255)                                                                                                                       gcATCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCa            <  1:1116928/132‑1 (MQ=255)                                                                                                                         aTCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCATTGAGTaaaa  >  1:616885/1‑140 (MQ=255)                                                                                                                         aTCCGGCATGAGCAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCATTGAGTaaaa  >  1:776935/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                 TGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAACAATGCGTACGTTGTCAACAATCTGCACCGCCGGTAACCCCGGCGGTTTTCTGTTTATGGCTCCTGATGAACAACTTCTGGCGGTGGAACGTCAACCAACTTTCTGCTTAACAACGCATTGAGTAAAA  >  NC_000913/1068325‑1068584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑