Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,604,632	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_pae_tpiA	4,604,632	0	C	A	100.0%	175.8 / NA	56	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (34/22);  total (34/22)

ACCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604487‑4604777                                                                                                                                                  |                                                                                                                                                  accgaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCGATGAAACAAACTTCTGAGCAGCTTAAACGCAATATTAAAACGATACGTGaaca                                                                                                                                                >  2:76650/1‑149 (MQ=255) accgaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGaaca                                                                                                                                                >  1:614158/1‑149 (MQ=255)   cgaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATa                                                                                                                                              >  2:643425/1‑149 (MQ=255)     accgacTGAACAATCAGGGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATaaa                                                                                                                                            <  1:378473/149‑1 (MQ=255)      ccgacTGAACAATAAGCGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAACCGAACCGTGAACATaact                                                                                                                                           >  2:270554/1‑147 (MQ=255)           tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGACATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAACCGCAATATCAAAACGCTCCGCGAACAGAAATTTAAt                                                                                                                                      >  2:12626/1‑149 (MQ=255)               cAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACAATCCGTGAACATAAATTTAAtgtca                                                                                                                                  >  2:70847/1‑147 (MQ=255)                aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                                 >  1:112016/1‑149 (MQ=255)                aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                                 >  2:38965/1‑149 (MQ=255)                  tCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAAAAATTTAATGTGATGt                                                                                                                               >  1:347898/1‑149 (MQ=255)                        gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTaa                                                                                                                                       >  2:379853/1‑135 (MQ=255)                        gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTaa                                                                                                                                       <  1:379853/135‑1 (MQ=255)                            aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGa                                                                                                                                  <  2:344052/136‑1 (MQ=255)                            aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGa                                                                                                                                  >  1:344052/1‑136 (MQ=255)                             ttcacaaaaGCGGGAAGTTAAGGTCGACGGAGAGAGAAATATTGCGCTTTAGGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    <  2:652656/143‑1 (MQ=255)                             ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    >  2:281019/1‑149 (MQ=255)                                  cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCGTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAAGATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAg                                                                                                               <  1:477706/149‑1 (MQ=255)                                   aaaGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGAAACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGt                                                                                                              >  2:230070/1‑149 (MQ=255)                                    aaGCCGGACGTCAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGtt                                                                                                             <  1:1823/149‑1 (MQ=255)                                        ccgaagTTAAGCCAGACGGAGAGAGAAATATTGCGCTTTATGGCGCGTGGTTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGa                                                                                                         <  2:453199/144‑1 (MQ=255)                                             gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTCATGTGATGTCGAAACTGGGCGTCAGTTCTCACGctg                                                                                                    >  1:287374/1‑147 (MQ=255)                                             gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGCAACTCGGCGTCAGTTCTGACGccg                                                                                                    >  2:478648/1‑147 (MQ=255)                                              ttAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAgg                                                                                                   <  1:643425/149‑1 (MQ=255)                                               gaaGCCCGAAGGAGAGAGAAATATTGCGCTTTATGTCGCGGGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAggg                                                                                                  <  1:593609/148‑1 (MQ=255)                                                 aGCACGACGAAGAGAGAAATATTGGTCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgtt                                                                                                <  1:494357/149‑1 (MQ=255)                                                    ccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAGGATAAATTTAATGTGATGTAGAAACTGGGCGTCAGTTCTGACGCAGGgttgtt                                                                                             >  1:460609/1‑149 (MQ=255)                                                    ccGACGGAGAGAGAAAGATTGCGGTGTGGGTCGGTTGGCTATTCTATGACACAAACTGCCGAGCAGCTTAAACGAAATAGCGAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACGGGGGGTCAGTTCTGATGCAGGgttgtt                                                                                             <  2:301200/149‑1 (MQ=255)                                                       aCGGGGAGAGAAATAGTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAAGCGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                          <  1:655452/149‑1 (MQ=255)                                                       aCGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACACAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCCAAACTAGGCGCCAGTTCTAACGCCGGGcttttgta                                                                                          >  2:512601/1‑147 (MQ=255)                                                         ggAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAgg                                                                                        <  1:281019/149‑1 (MQ=255)                                                           agagagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGcc                                                                                      >  1:286500/1‑149 (MQ=255)                                                            gagagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCg                                                                                     >  2:675152/1‑149 (MQ=255)                                                             agagaAATATTGCGCTTTATGTCGCGTGGCTACTCCATTACACAAATTGCCGAGCAGCTTAAACACAATATCAAAACGAACCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGc                                                                                    >  1:31727/1‑149 (MQ=255)                                                              gagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCa                                                                                   <  2:1405/149‑1 (MQ=255)                                                                     atTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                            >  1:268949/1‑149 (MQ=255)                                                                          gcTTTATGTGGGGTGGCTACTGAATGGCAGAAATTGGCGAGCAGCTTAAAGGCAATATCAAAACGATCCGTGAACATGAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                       <  2:231671/149‑1 (MQ=255)                                                                          gcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGAGGCCGGGTTGTTGGGGGCCGCCGATATTCTGtaa                                                                       >  1:630825/1‑147 (MQ=255)                                                                            tttATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatg                                                                     >  1:562057/1‑149 (MQ=255)                                                                               aTGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatgtat                                                                  >  1:426543/1‑149 (MQ=255)                                                                                        tgCTAATCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTg                                                         <  2:462502/148‑1 (MQ=255)                                                                                        agatACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTg                                                         <  2:55994/146‑1 (MQ=255)                                                                                              tCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTGATGTATGCGGCATTGCGAAAc                                                   >  1:442690/1‑149 (MQ=255)                                                                                                    acacAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTaa                                             >  2:453819/1‑149 (MQ=255)                                                                                                    acacAAATTGCCGAGCAGCTAAAACGCAATAGCAAAACGATGCGTGAAAATAAATTTAATGTGAGAGCGAAACTGGGCGTCAGTTCTGACGCAGGGATGTTGGGGTCCGCAGATACTCTATTACGTCTGCGGCCTTCCTAACCAAGGaa                                             >  2:650874/1‑149 (MQ=255)                                                                                                     gacaAATTGCCGAGCAGCTTAAACGGAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGTTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAt                                            <  2:408387/148‑1 (MQ=255)                                                                                                        aaaTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtgtg                                         >  1:242171/1‑149 (MQ=255)                                                                                                              cctagcagcTTAAACGAAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCAt                                   <  1:148538/146‑1 (MQ=255)                                                                                                               cGAGCAGCTTAAACGCAATATCAATACGTTCCGTGAGCATAGATTTAATGGGATTTCGACACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATc                                  <  1:12626/149‑1 (MQ=255)                                                                                                               cGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATc                                  >  1:646110/1‑149 (MQ=255)                                                                                                                  gcagcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCt                               <  2:614158/149‑1 (MQ=255)                                                                                                                        tAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAGACAAGTAATGTGTTGCATCCCTATTAAt                         >  2:637748/1‑149 (MQ=255)                                                                                                                           aCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGACACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTCCTCCg                      >  2:35956/1‑149 (MQ=255)                                                                                                                            cGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGc                     >  1:78081/1‑149 (MQ=255)                                                                                                                                   tCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGc              >  2:321119/1‑149 (MQ=255)                                                                                                                                     aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg            >  1:459521/1‑149 (MQ=255)                                                                                                                                      aaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCgg           >  1:73159/1‑149 (MQ=255)                                                                                                                                      aaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCgg           <  1:230070/149‑1 (MQ=255)                                                                                                                                               gTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGATGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTc  >  2:175623/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  ACCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604487‑4604777

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: ‑