Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,737,713	(G)6→5	intergenic (+67/‑32)	pheL → / → pheA	phe operon leader peptide/fused chorismate mutase/prephenate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,737,708	0	G	.	100.0%	229.2 / NA	53	intergenic (+62/‑37)	pheL/pheA	phe operon leader peptide/fused chorismate mutase/prephenate dehydratase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (27/26);  total (27/26)

GTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGCC  >  NC_000913/2737572‑2737840                                                                                                                                         |                                                                                                                                     gtactAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggg                                                                                                                                   <  2:447620/140‑1 (MQ=255)   actAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggggc                                                                                                                                 <  2:969585/140‑2 (MQ=255)     tAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggggcct                                                                                                                               >  1:998608/1‑137 (MQ=255)       aaGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCttt                                                                                                                            >  1:308416/1‑140 (MQ=255)         gTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCttttt                                                                                                                          >  2:750011/1‑140 (MQ=255)          tCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCtttttt                                                                                                                         >  1:53377/1‑140 (MQ=255)          tCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCtttttt                                                                                                                         >  2:1195193/1‑140 (MQ=255)            aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  1:1170933/1‑140 (MQ=255)            aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  2:556808/1‑140 (MQ=255)            aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  2:87838/1‑140 (MQ=255)                aaGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   <  1:750011/140‑1 (MQ=255)                   gAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAAc                                                                                                                >  1:223910/1‑140 (MQ=255)                   gAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAAc                                                                                                                >  1:866568/1‑140 (MQ=255)                     aacaaacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACaa                                                                                                              <  1:99464/140‑1 (MQ=255)                         aacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAg                                                                                                          <  2:338658/140‑1 (MQ=255)                         aacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAg                                                                                                          <  1:1195193/140‑1 (MQ=255)                          acaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         <  2:775821/140‑1 (MQ=255)                          acaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCC‑TTTTTATTGATAACAAAAAGGc                                                                                                        <  2:1172540/140‑1 (MQ=255)                           caTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGc                                                                                                        <  2:629645/140‑1 (MQ=255)                             tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   >  2:117369/1‑127 (MQ=255)                             tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   <  1:117369/127‑1 (MQ=255)                             tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  2:843/140‑1 (MQ=255)                             tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  1:419507/140‑1 (MQ=255)                             tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  1:24485/140‑1 (MQ=255)                              gAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAac                                                                                                     <  2:590802/140‑1 (MQ=255)                                  cacaTACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTa                                                                                                 <  2:234960/140‑1 (MQ=255)                                        ccGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACAt                                                                                           >  1:994496/1‑140 (MQ=255)                                         cGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         <  2:1034314/125‑1 (MQ=255)                                         cGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         >  1:1034314/1‑125 (MQ=255)                                             tttCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGaa                                                                                      <  2:308416/140‑1 (MQ=255)                                               tcttcGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGaaaa                                                                                    >  1:302038/1‑140 (MQ=255)                                                   cGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCg                                                                                >  2:520596/1‑140 (MQ=255)                                                   cGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCg                                                                                >  1:497576/1‑140 (MQ=255)                                                              ttACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCt                                                                     <  1:58931/140‑1 (MQ=255)                                                                aCCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGc                                                                   <  2:223910/140‑1 (MQ=255)                                                                    tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  2:246925/1‑140 (MQ=255)                                                                    tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  1:287082/1‑140 (MQ=255)                                                                    tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  1:586495/1‑140 (MQ=255)                                                                     ccccTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCACAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgagag                                                              >  2:1074957/1‑140 (MQ=255)                                                                      cccTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgagaga                                                             >  2:401506/1‑140 (MQ=255)                                                                                gAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgc                                                   >  2:595743/1‑140 (MQ=255)                                                                                 aGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgcg                                                  <  2:998608/140‑1 (MQ=255)                                                                                  ggCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgcgc                                                 <  2:586495/140‑1 (MQ=255)                                                                                      tttCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGa                                             >  1:358549/1‑140 (MQ=255)                                                                                           tcgtGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGaaa                                        <  1:556808/140‑1 (MQ=255)                                                                                                   aaCAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:232731/140‑1 (MQ=255)                                                                                                     cAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGc                              <  2:287082/140‑1 (MQ=255)                                                                                                      aGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCg                             <  2:994496/140‑1 (MQ=255)                                                                                                       gAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAattatcatcca                            <  2:358549/140‑7 (MQ=255)                                                                                                        aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                >  1:274124/1‑135 (MQ=255)                                                                                                        aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                >  1:840887/1‑135 (MQ=255)                                                                                                        aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:274124/135‑1 (MQ=255)                                                                                                        aaTGCGAAGACCAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACCCTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:840887/135‑1 (MQ=255)                                                                                                                  cGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGaa                 >  2:622079/1‑140 (MQ=255)                                                                                                                  cGAACAATAAGGCCTACCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGaa                 >  1:269922/1‑140 (MQ=255)                                                                                                                                 cccAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGcc  >  1:619093/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                     GTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGCC  >  NC_000913/2737572‑2737840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑