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%	179.0 / NA	55	*393* (TAG→TAA)	xylR	xylose divergent operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/27);  total (28/27)

CCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGC‑G‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA  >  NC_000913/3736024‑3736287                                                                                                                                      |                                                                                                                                     ccaccTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑g‑aat                                                                                                                               <  1:366789/139‑3 (MQ=255)              cAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTc                                                                                                                   <  2:656382/139‑1 (MQ=255)              cAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTc                                                                                                                   <  1:259499/139‑1 (MQ=255)               aaTGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCg                                                                                                                  >  1:543634/1‑139 (MQ=255)                  gagaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCg                                                                                                               <  1:727202/139‑1 (MQ=255)                  gagaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCg                                                                                                               <  2:307030/139‑1 (MQ=255)                   agaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGt                                                                                                              >  2:324959/1‑139 (MQ=255)                       atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGCCGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          <  1:659108/139‑1 (MQ=255)                       atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          >  1:785969/1‑139 (MQ=255)                         cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACTCGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGGGAATTGTCGGCGTcaca                                                                                                          >  1:523237/1‑137 (MQ=255)                         cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          <  2:523237/137‑1 (MQ=255)                         cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATc                                                                                                        >  1:44911/1‑139 (MQ=255)                             aaTGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGt                                                                                                    >  2:531547/1‑139 (MQ=255)                               tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                                  <  1:364098/139‑1 (MQ=255)                               tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                                  <  1:531547/139‑1 (MQ=255)                                      ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                           <  2:72221/139‑1 (MQ=255)                                        aTCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTg                                                                                         >  1:180266/1‑139 (MQ=255)                                                   cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg                                                                              >  2:780014/1‑139 (MQ=255)                                                   cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg                                                                              >  1:558671/1‑139 (MQ=255)                                                            tACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGaa                                                                     <  1:324959/139‑1 (MQ=255)                                                             aCTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAAc                                                                    >  1:167458/1‑139 (MQ=255)                                                             aCTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAAc                                                                    >  1:287918/1‑139 (MQ=255)                                                              ctctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACg                                                                   <  2:167458/139‑1 (MQ=255)                                                                ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          >  1:132333/1‑98 (MQ=255)                                                                ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          <  2:132333/98‑1 (MQ=255)                                                                  gTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCtt                                                               >  2:706325/1‑139 (MQ=255)                                                                   tttttAAAAAAGCATATGACACGACGCCAAAAGAGTATTGCGAAGTAAATAGCGAGGTGATGTTGTAAC‑GAATGATGAGAATTGTCTGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCttc                                                              >  2:662750/1‑138 (MQ=255)                                                                       tAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCg                                                          <  2:558671/139‑1 (MQ=255)                                                                           aaaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt                                                      <  2:785969/139‑1 (MQ=255)                                                                            aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                     <  1:780014/139‑1 (MQ=255)                                                                            aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCGGCGTGGATGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                     <  1:535212/139‑1 (MQ=39)                                                                                  atGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                               <  1:212300/139‑1 (MQ=255)                                                                                  atGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                               <  2:719345/139‑1 (MQ=255)                                                                                         gacgCCAAAAGAGTATCGCGATGTAAATAGCGGGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATg                                        >  1:475708/1‑139 (MQ=255)                                                                                         gacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATg                                        >  1:594011/1‑139 (MQ=255)                                                                                            gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt                                                      >  1:355225/1‑122 (MQ=255)                                                                                            gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt                                                      <  2:355225/122‑1 (MQ=255)                                                                                                       aTCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaa                          >  1:546439/1‑139 (MQ=255)                                                                                                        tCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          <  2:466233/58‑1 (MQ=255)                                                                                                        tCGCGATGTAAATAGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTcaca                                                                                                          >  1:466233/1‑58 (MQ=255)                                                                                                                  aaTAGCGGGGTCATGTTGTAACGG‑ATGATGAGAATTGGCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCGTTATCCGACCTACCCGCCAGGCATGAGAAAACGCACCAACAACGCTTCAg               <  1:662750/139‑1 (MQ=39)                                                                                                                     aGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCt            >  2:724978/1‑139 (MQ=255)                                                                                                                     aGCGAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCt            <  1:504032/139‑1 (MQ=255)                                                                                                                        gAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                                  >  1:719759/1‑50 (MQ=255)                                                                                                                        gAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                                  <  2:719759/50‑1 (MQ=255)                                                                                                                        gAGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGt         >  1:741106/1‑139 (MQ=255)                                                                                                                         aGGTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTa        >  1:427575/1‑139 (MQ=255)                                                                                                                          ggTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  2:654891/1‑139 (MQ=255)                                                                                                                          ggTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  1:400125/1‑139 (MQ=255)                                                                                                                          ggTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  2:358320/1‑139 (MQ=255)                                                                                                                          ggTCATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTACGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg       >  1:17362/1‑139 (MQ=255)                                                                                                                             cATGTTGTAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTc    <  1:724978/139‑1 (MQ=255)                                                                                                                               tgttgtAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa  <  2:287918/139‑1 (MQ=255)                                                                                                                               tgttgtAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa  >  2:236044/1‑139 (MQ=255)                                                                                                                               tgttgtAAC‑GAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa  <  2:180266/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                     CCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGC‑G‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA  >  NC_000913/3736024‑3736287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑