Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,729,347	G→A	E337K (GAG→AAG)	xylR →	xylose divergent operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,729,347	0	G	A	100.0%	234.8 / NA	68	E337K (GAG→AAG)	xylR	xylose divergent operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (38/30);  total (38/30)

TCCAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCGAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATCGCA  >  CP009273/3729284‑3729411                                                                |                                                                 tCCAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGaa                                                              <  1:2143283/68‑1 (MQ=255) tCCAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGaa                                                              >  1:1133634/1‑68 (MQ=255) tCCAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGaa                                                              <  1:4615874/68‑1 (MQ=255)   cAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGc                                                            <  1:1096062/68‑1 (MQ=255)     aTCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTg                                                          <  1:3132704/68‑1 (MQ=255)       cTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGga                                                        >  1:475700/1‑68 (MQ=255)       cTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGga                                                        >  1:1586334/1‑68 (MQ=255)       cTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGga                                                        >  1:4142846/1‑68 (MQ=255)       cTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGga                                                        >  1:3745255/1‑68 (MQ=255)         tGAGAAGCGTTTTAAAGAAGAGGTGGTTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGgaga                                                      >  1:1492802/1‑68 (MQ=255)         tGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGgaga                                                      >  1:480749/1‑68 (MQ=255)            gaAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAg                                                   >  1:5177661/1‑68 (MQ=255)            gaAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAg                                                   >  1:1412504/1‑68 (MQ=255)                cGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAgcgcg                                               >  1:1932327/1‑68 (MQ=255)                   tttAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAg                                            <  1:2305236/68‑1 (MQ=255)                    ttAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGt                                           <  1:4149672/68‑1 (MQ=255)                     tAAAGAAGAGGTGGGTGAAACCATCCATGCGATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTc                                          <  1:3518556/68‑1 (MQ=255)                      aaaGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTct                                         >  1:5323007/1‑68 (MQ=255)                      aaaGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTct                                         <  1:954940/68‑1 (MQ=255)                      aaaGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTct                                         >  1:3167606/1‑68 (MQ=255)                       aagaagAGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTctg                                        <  1:1541663/68‑1 (MQ=255)                        agaagaGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTctgc                                       >  1:5175125/1‑68 (MQ=255)                        agaagaGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTctgc                                       >  1:211552/1‑68 (MQ=255)                         gaagaGGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTCGAGAAAGCGCGCTGTctgct                                      >  1:2175936/1‑68 (MQ=255)                           tgagGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGa                                    <  1:883250/67‑1 (MQ=255)                           agagGTGGGTGAAACCATCCATGCCATGCTTCAAGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGa                                    <  1:3458711/68‑1 (MQ=255)                             agGTGGGTGAAACCATGCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGAtt                                  >  1:1957130/1‑68 (MQ=255)                             agGTGGGTGAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGAtt                                  >  1:2201137/1‑68 (MQ=255)                                tgggtgACACCATCCATGCCCTGATTCATGCAAAGCAGCTGGAGCAAGCGCGCAGTCTGCTGATTTCa                               >  1:4744409/1‑68 (MQ=255)                                tgggtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCa                               <  1:2580238/68‑1 (MQ=255)                                tgggtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCa                               >  1:5138648/1‑68 (MQ=255)                                tgggtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCa                               <  1:4720210/68‑1 (MQ=255)                                tgggtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCa                               >  1:4710939/1‑68 (MQ=255)                                   gtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAacc                            >  1:64697/1‑68 (MQ=255)                                   gtgAAACCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAacc                            >  1:5452288/1‑68 (MQ=255)                                        aCCATCCATGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCtt                       >  1:5625860/1‑68 (MQ=255)                                         ccatccatGCCATGATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTg                      >  1:497189/1‑68 (MQ=255)                                          catccatGCCATGATTCATGCCAAGAAGCTGGAGAAACCGCGCAGTCTGCTGATTTCAACCACCTTGt                     <  1:580418/68‑1 (MQ=255)                                             ccatgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGa                  >  1:5210174/1‑68 (MQ=255)                                              catgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGAt                 <  1:550015/68‑1 (MQ=255)                                              catgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGAt                 <  1:122826/68‑1 (MQ=255)                                               atgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATc                <  1:2104777/68‑1 (MQ=255)                                                tgccatgATTCATGCCAAGAAGCTTGAGAAAGCTCGAAGTCTGCTGATTTCAACCAACTTGTCGATCa               >  1:3765711/1‑68 (MQ=255)                                                tgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCa               <  1:1082136/68‑1 (MQ=255)                                                tgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCa               <  1:555745/68‑1 (MQ=255)                                                tgccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCa               <  1:2877576/68‑1 (MQ=255)                                                 gccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCaa              >  1:3001134/1‑68 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCACCCACCTTGTCGATCAAt             >  1:3899368/1‑68 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAAt             <  1:119244/68‑1 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAAt             >  1:931985/1‑68 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAAt             <  1:5482521/68‑1 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAAt             <  1:773771/68‑1 (MQ=255)                                                  ccatgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAAt             >  1:3587211/1‑68 (MQ=255)                                                  ccatgATTCATGCAAAGAAGCTGGATAAAGCGCGCAGTCTTCTGATTTCAACCACCTTGTCGATCAAt             <  1:4024580/68‑1 (MQ=255)                                                  ccatgAATCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCCATCAAt             <  1:5518833/68‑1 (MQ=255)                                                   catgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATg            >  1:1149274/1‑68 (MQ=255)                                                     tgATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATgag          <  1:1879914/68‑1 (MQ=255)                                                      gATTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATgaga         <  1:709528/68‑1 (MQ=255)                                                       aTTCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGat        >  1:835555/1‑68 (MQ=255)                                                        ttCATGCCAAGAAGCTGGAGAACGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGata       >  1:2207624/1‑68 (MQ=255)                                                         tCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGatat      >  1:3326922/1‑68 (MQ=255)                                                         tCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGatat      >  1:2447285/1‑68 (MQ=255)                                                         tCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGatat      >  1:903532/1‑68 (MQ=255)                                                         tCATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGAGCAAGGAGatat      >  1:5072353/1‑68 (MQ=255)                                                          cATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATc     <  1:4164841/68‑1 (MQ=255)                                                          cATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATc     <  1:4506951/68‑1 (MQ=255)                                                          cATGCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATc     <  1:3506134/68‑1 (MQ=255)                                                             gCCAAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATCGCa  >  1:3253954/1‑68 (MQ=255)                                                                |                                                                 TCCAATCTTGAGAAGCGTTTTAAAGAAGAGGTGGGTGAAACCATCCATGCCATGATTCATGCCGAGAAGCTGGAGAAAGCGCGCAGTCTGCTGATTTCAACCACCTTGTCGATCAATGAGATATCGCA  >  CP009273/3729284‑3729411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑