Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,736,157	G→A	*393* (TAG→TAA)	xylR →	xylose divergent operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,736,157	0	G	A	100.0%	202.7 / NA	63	*393* (TAG→TAA)	xylR	xylose divergent operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (33/30);  total (33/30)

AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑A‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA  >  NC_000913/3736022‑3736287                                                                                                                                        |                                                                                                                                     aaCCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑a                                                                                                                                  >  1:3371/1‑139 (MQ=255) aaCCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑a                                                                                                                                  >  2:224798/1‑139 (MQ=255)       cTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAa‑tgatg                                                                                                                            >  1:605902/1‑139 (MQ=255)       cTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAa‑tgatg                                                                                                                            >  2:691831/1‑139 (MQ=255)        ttGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑tgatga                                                                                                                           >  1:564708/1‑139 (MQ=255)               tCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGt                                                                                                                    <  1:642869/139‑1 (MQ=255)                    gagaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCg                                                                                                               <  1:224798/139‑1 (MQ=255)                         atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          >  2:908450/1‑139 (MQ=255)                         atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          >  2:842100/1‑139 (MQ=255)                         atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          >  1:371246/1‑139 (MQ=255)                         atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          <  2:257485/139‑1 (MQ=255)                           cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATc                                                                                                        >  2:231155/1‑139 (MQ=255)                                 tgttCGGTTATCAATCGCTGCAATATATCAACTCTGTTATTAAAAAAGCATATGACACGACGACAAAAGAGCATCGAGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAAAAGTGTCGGCCTCAAATCAGGTaa                                                                                                  <  2:482152/139‑1 (MQ=255)                                        ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                           <  2:391307/139‑1 (MQ=255)                                        ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                           <  1:433496/139‑1 (MQ=255)                                        ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                           <  1:231155/139‑1 (MQ=255)                                         tATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGt                                                                                          <  2:3371/139‑1 (MQ=255)                                           tCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                        >  2:20638/1‑139 (MQ=255)                                                  cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          >  2:814999/1‑114 (MQ=255)                                                  cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          <  1:814999/114‑1 (MQ=255)                                                  cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTGACGCTGCGTGGTTGTCgg                                                                                 >  2:985597/1‑139 (MQ=255)                                                     cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg                                                                              >  1:530637/1‑139 (MQ=255)                                                            tCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTGACGCTGCGTGGTTGTCGGATGCGGCGTg                                                                       <  1:985597/139‑1 (MQ=255)                                                             cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGa                                                                      >  1:539236/1‑139 (MQ=255)                                                             cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACG‑AGTGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGa                                                                      >  2:562009/1‑139 (MQ=255)                                                                ctctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACg                                                                   <  2:787207/139‑1 (MQ=255)                                                                 tctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc                                                                  <  1:691831/139‑1 (MQ=255)                                                                   tGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCt                                                                >  1:196037/1‑139 (MQ=255)                                                                     tttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTc                                                                                                                   <  1:262567/86‑1 (MQ=255)                                                                     tttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTc                                                                                                                   >  2:262567/1‑86 (MQ=255)                                                                     tttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTa                                                              >  1:357686/1‑139 (MQ=255)                                                                              aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                     <  1:20638/139‑1 (MQ=255)                                                                              aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                     <  1:842100/139‑1 (MQ=255)                                                                               aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                            <  1:684766/115‑1 (MQ=255)                                                                               aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                            >  2:684766/1‑115 (MQ=255)                                                                                    atGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                               <  2:290252/139‑1 (MQ=255)                                                                                             cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑aatgat                                                                                                                             >  1:294804/1‑47 (MQ=255)                                                                                             cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑aatgat                                                                                                                             <  2:294804/52‑6 (MQ=255)                                                                                             cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                               >  1:694128/1‑130 (MQ=255)                                                                                             cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                               <  2:694128/130‑1 (MQ=255)                                                                                              gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                        >  1:261944/1‑88 (MQ=255)                                                                                              gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                        <  2:261944/88‑1 (MQ=255)                                                                                               ccAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaa                                    <  2:885249/139‑1 (MQ=255)                                                                                               ccAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaa                                    <  1:562009/139‑1 (MQ=255)                                                                                                cAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaa                                   >  2:963247/1‑139 (MQ=255)                                                                                                 aaaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                                  <  1:588452/139‑1 (MQ=255)                                                                                                       gTATCGCGATGTAAATAGCGAGGTCATGTTGTGACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCAcc                            >  2:639614/1‑139 (MQ=255)                                                                                                            gcgATGTACATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTATCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                       <  1:639614/139‑1 (MQ=39)                                                                                                               aTGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                            >  2:956501/1‑83 (MQ=255)                                                                                                               aTGTAAATAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                            <  1:956501/83‑1 (MQ=255)                                                                                                                     aTAGCGAGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAgg              >  1:559395/1‑139 (MQ=255)                                                                                                                           aGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                       >  1:861974/1‑124 (MQ=255)                                                                                                                           aGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                       <  2:861974/124‑1 (MQ=255)                                                                                                                           aGGTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTa        >  1:391039/1‑139 (MQ=255)                                                                                                                            ggTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                       <  1:558320/123‑1 (MQ=255)                                                                                                                            ggTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                       >  2:558320/1‑123 (MQ=255)                                                                                                                            ggTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  2:442745/1‑139 (MQ=255)                                                                                                                            ggTCATGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  2:107389/1‑139 (MQ=255)                                                                                                                                aTGTTGTAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCa   >  1:383447/1‑139 (MQ=255)                                                                                                                                 tgttgtAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          >  1:751426/1‑35 (MQ=255)                                                                                                                                 tgttgtAACGAA‑TGATGAGAATTGTCGGCGTcaca                                                                                                          <  2:751426/35‑1 (MQ=255)                                                                                                                                 tgttgtAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa  <  2:605902/139‑1 (MQ=255)                                                                                                                                 tgttgtAACGAA‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa  <  2:539236/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                     AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑A‑TGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA  >  NC_000913/3736022‑3736287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑