Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_tpiA	4,604,746	C→A	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_tpiA	4,604,746	0	C	A	100.0%	194.1 / NA	60	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (26/34);  total (26/34)

GACCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_vch_tpiA/4604600‑4604891                                                                                                                                                   |                                                                                                                                                  gaccgaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGCCGTTAAGCCCGACGGAGAGAGCAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATAAAACCGATCTGTGaac                                                                                                                                                 >  1:162980/1‑149 (MQ=255)       ccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGCCGTTAAGCCCGACGGAGAGAGCAATGTTGCGCTTTATGTGGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAAt                                                                                                                                           <  2:963681/149‑1 (MQ=255)           cTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTaa                                                                                                                                       <  2:319729/149‑1 (MQ=255)            tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                      >  2:66190/1‑149 (MQ=255)            tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                      <  2:353332/149‑1 (MQ=255)              aaCAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAAACATTTAAtgt                                                                                                                                    >  2:343445/1‑149 (MQ=255)                 aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                                 <  1:66190/149‑1 (MQ=255)                 aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                                 >  1:581776/1‑149 (MQ=255)                    cAGTGGTACATTAACCAAAGCCGGGCGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTc                                                                                                                              <  2:816319/149‑1 (MQ=255)                    cAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTc                                                                                                                              <  1:280596/149‑1 (MQ=255)                        ggTACATTAACCAAAGCCGGACGTTAAGCCCGATGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaaa                                                                                                                          <  1:754616/149‑1 (MQ=255)                                  ccAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCACGTGGCTACTGAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTcc                                                                                                                >  2:698131/1‑148 (MQ=255)                                   cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTCGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTAAACATAAATTTAATGTGATATCGAAACTggggccccg                                                                                                               >  2:481043/1‑143 (MQ=255)                                   cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTAGAATGGCGACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGAGTCAg                                                                                                               >  1:985249/1‑149 (MQ=255)                                               ttAAGCCCGACGGAGCGAGAAACATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAgg                                                                                                   <  1:20723/149‑1 (MQ=255)                                                    cccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgt                                                                                              <  1:348134/149‑1 (MQ=255)                                                    cccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgt                                                                                              <  1:662491/149‑1 (MQ=255)                                                      cGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGTTGTCGAAACTGGGCGTCAGTTCTGACGCAGGGttgttg                                                                                            <  2:917679/149‑1 (MQ=255)                                                      cGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGa                                                                                                         >  2:760166/1‑136 (MQ=255)                                                      cGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGa                                                                                                         <  1:760166/136‑1 (MQ=255)                                                        aCGGAGATAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                          <  1:201020/149‑1 (MQ=255)                                                         atctgagagaAATATTGCGTTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGCGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTCGGac                                                                                         <  1:990116/145‑2 (MQ=255)                                                           gagagagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGAACTGACGccc                                                                                                    >  2:749731/1‑134 (MQ=255)                                                           gagagagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGAACTGACGccc                                                                                                    <  1:749731/136‑3 (MQ=255)                                                              agagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACGCAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTACTGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAggggat                                                                                    >  2:990116/1‑145 (MQ=255)                                                                agaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAg                                                                                  >  2:131250/1‑149 (MQ=255)                                                                  aaaTATTGCGCTTTATGTCGCGTGGCTACTCAATGACCCAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAATGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGAAGat                                                                                >  1:484292/1‑149 (MQ=255)                                                                   aaTATGGCGCTTTATTTCGCGGGGCTACTCAATGACACAAATTGCCGAGTAGCTTAAACGCAATATCAAAACGAGCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGata                                                                               <  1:846644/149‑1 (MQ=255)                                                                        tGCGCTTTATGTCGCTTGGCTACGCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCCATTCTGACGCAGGGTTTTTGGAGGCCGCCGATATTcgt                                                                          >  2:390227/1‑147 (MQ=255)                                                                        tGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAACCTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGCTATTcgg                                                                          >  2:695665/1‑147 (MQ=255)                                                                            cTTTATGTCGCGTGGCTACTCAATGACACAAATTCCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCCCAGATATACTGTtat                                                                      >  2:262633/1‑149 (MQ=255)                                                                                     gcgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTg                                                                                                                       <  2:848161/91‑1 (MQ=255)                                                                                     gcgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTg                                                                                                                       >  1:848161/1‑91 (MQ=255)                                                                                        tGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTgg                                                                                                                      <  2:111442/89‑1 (MQ=255)                                                                                        tGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTgg                                                                                                                      >  1:111442/1‑89 (MQ=255)                                                                                         gccTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTg                                                         <  2:864994/147‑1 (MQ=255)                                                                                           ggacgcAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCg                                                       <  1:235851/144‑1 (MQ=255)                                                                                            tACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGa                                                      <  1:131250/149‑1 (MQ=255)                                                                                              cTCAATGACACAACTTGCCGAGCAGCTTAAACGGAATATCAAAACGCTCGGTGAACATAAATTTGATGGAATGTCGACCCCGGGCGTCAGGTCTGCCGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                    <  2:845917/149‑1 (MQ=255)                                                                                               tCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATTAAAACGATCCATGAACATAAATTTAATGTAAAGTCTGAAATGGGGGTCAGTTCTGACGCAGGGGTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAAc                                                   >  2:137088/1‑149 (MQ=255)                                                                                                 aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACTATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGata                                                                               <  2:723991/119‑1 (MQ=255)                                                                                                 aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACTATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGata                                                                               >  1:723991/1‑119 (MQ=255)                                                                                                 aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                                 >  2:851286/1‑149 (MQ=255)                                                                                                     acacAAATTGCCGAGCAGCTTAAAGGAAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTaa                                             <  2:484292/149‑1 (MQ=255)                                                                                                     acacAAATTGACGAGCAGCTTAAACGTAATATCAAAACGAGCCGTGAAAATAAATTTAATGTGATGTCGAAACTTGGCGTCAGTTCTGTCGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTaa                                             <  2:863683/149‑1 (MQ=255)                                                                                                          aaTTGCCAACCATCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATgtgt                                        <  1:798472/149‑1 (MQ=255)                                                                                                           agtGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                       <  1:483358/147‑1 (MQ=255)                                                                                                           aTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                       >  1:445982/1‑149 (MQ=255)                                                                                                           aTTGCCGAGCAGCTTAAACGCAATACCAAAGCGATCCGTGAACGTAAATTTAATGTGATGTCGAAACTGGGCTTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                       <  2:923615/149‑1 (MQ=255)                                                                                                                         tAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                            <  1:386649/98‑1 (MQ=255)                                                                                                                         tAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                            >  2:386649/1‑98 (MQ=255)                                                                                                                           aaCTCAATATCAAAACGTTCCTTGAACATAATTTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATcc                       <  1:3093/149‑1 (MQ=255)                                                                                                                              gCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGAGTGGCATCCCTATTAATCTGCa                    >  1:238016/1‑149 (MQ=255)                                                                                                                                    tCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGc                                                                <  2:643750/99‑1 (MQ=255)                                                                                                                                    tCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGc                                                                >  1:643750/1‑99 (MQ=255)                                                                                                                                    tCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTACAGTGTAGGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGc              >  1:1023109/1‑149 (MQ=255)                                                                                                                                      aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGAAGGGACCATGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg            >  1:559078/1‑149 (MQ=255)                                                                                                                                      aaaaAGATCCGTGAAAATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg            <  1:861283/149‑1 (MQ=255)                                                                                                                                       aaaCGATCCGTGAACCTAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCgg           <  1:343445/149‑1 (MQ=255)                                                                                                                                                gTGAACATAAATTTAATGTGATTTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTc  <  2:541227/149‑1 (MQ=255)                                                                                                                                                gTGAACATAAATTTAATGTGATGTCGAAACGGGGCGTCAGTTCTGACGCAGAGTTGTTGGAGGCCGCAGATATTATGATATGTATGCGGCATTGCGAAATAAGTAATGTGTTGCATCCCTATTATGCCGCATAATGCTGGGTTTACCTc  >  2:670488/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                  GACCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_vch_tpiA/4604600‑4604891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑