Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	88,006	A→G	intergenic (+158/‑22)	ilvH → / → cra	acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	88,006	0	A	G	100.0%	215.2 / NA	60	intergenic (+158/‑22)	ilvH/cra	acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (39/21);  total (39/21)

CATGTCACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTACATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGAAAAAGTCA  >  NC_000913/87880‑88142                                                                                                                               |                                                                                                                                         cATGTCACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAg                                                                                                                             >  1:1003662/1‑140 (MQ=255)     tCACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGc                                                                                                                         <  2:1165072/140‑1 (MQ=255)     gcACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGc                                                                                                                         <  1:563405/139‑1 (MQ=255)      cACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATGTTACGCAAGGGGCa                                                                                                                        >  2:1211384/1‑140 (MQ=255)           tGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGAGGCAATtgt                                                                                                                   >  1:1280639/1‑140 (MQ=255)                          aaaTCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACt                                                                                                             >  2:438133/1‑131 (MQ=255)                          aaaTCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACt                                                                                                             <  1:438133/131‑1 (MQ=255)                            aTCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCg                                                                                                  <  1:1211384/140‑1 (MQ=255)                             tCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGc                                                                                                 >  1:249143/1‑140 (MQ=255)                              cAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCt                                                                                                <  2:975223/140‑1 (MQ=255)                                        cTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCgg                                                                                      >  2:786459/1‑140 (MQ=255)                                           gAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAg                                                                                   >  2:759430/1‑140 (MQ=255)                                           gAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAg                                                                                   >  1:897372/1‑140 (MQ=255)                                                 aaGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTcgc                                                                             >  1:812092/1‑140 (MQ=255)                                                  aGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTcgcg                                                                            <  1:1373872/140‑1 (MQ=255)                                                  aGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTcgcg                                                                            <  2:812092/140‑1 (MQ=255)                                                  aGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTcgcg                                                                            <  1:1332681/140‑1 (MQ=255)                                                     aGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGAc                                                                         <  1:759430/140‑1 (MQ=255)                                                      gTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGAcc                                                                        >  1:1341307/1‑140 (MQ=255)                                                      gTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGAc                                                                         <  2:50893/139‑1 (MQ=255)                                                      gTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGAc                                                                         >  1:50893/1‑139 (MQ=255)                                                         gCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACt                                                                     >  2:77714/1‑140 (MQ=255)                                                         gCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACt                                                                     >  2:169628/1‑140 (MQ=255)                                                         gCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACt                                                                     <  1:565716/140‑1 (MQ=255)                                                         gCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTAGCGGACCACt                                                                     <  2:114612/140‑1 (MQ=255)                                                           cGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGc                                                                   >  2:855540/1‑140 (MQ=255)                                                            gCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCa                                                                  <  2:1015658/140‑1 (MQ=255)                                                             cAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCaa                                                                 >  1:1305916/1‑140 (MQ=255)                                                                         tGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGttatta                                                     >  1:1113652/1‑140 (MQ=255)                                                                          gcgcTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTaa                                                    >  2:754035/1‑140 (MQ=255)                                                                               tAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCa                                               <  1:940770/140‑1 (MQ=255)                                                                                    gTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCg                                          <  2:296008/140‑1 (MQ=255)                                                                                        aTGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGc                                      >  2:1061029/1‑140 (MQ=255)                                                                                          gAATTTAACCCATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCaa                                    <  2:249143/140‑1 (MQ=255)                                                                                                   ccATACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGGAGCAATACCGtgtg                           <  2:1341307/140‑1 (MQ=255)                                                                                                     aTACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAg                         >  2:557375/1‑140 (MQ=255)                                                                                                      tACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAg                         <  1:375719/139‑1 (MQ=255)                                                                                                      tACCAGTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGGGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAg                         >  2:375719/1‑139 (MQ=255)                                                                                                           gTACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACaa                   >  1:91310/1‑140 (MQ=255)                                                                                                            tACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCaa                                    >  1:1298613/1‑122 (MQ=255)                                                                                                            tACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCaa                                    <  2:1298613/122‑1 (MQ=255)                                                                                                            tACAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACaaa                  >  1:1258045/1‑140 (MQ=255)                                                                                                             aCAATGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACaaaa                 >  2:588309/1‑140 (MQ=255)                                                                                                                aTGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCg              >  1:504437/1‑140 (MQ=255)                                                                                                                aTGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCg              >  1:1359390/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGGGGGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  1:1359493/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  2:1379308/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  1:1139112/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  1:424008/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  1:1149411/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  2:774184/1‑140 (MQ=255)                                                                                                                 tGGCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGCGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGt             >  2:896085/1‑140 (MQ=255)                                                                                                                   gCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTGACGGCAAAGCGAAGCAATACCGTGTGAGCGACaa                   <  1:659504/132‑1 (MQ=255)                                                                                                                   gCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTGACGGCAAAGCGAAGCAATACCGTGTGAGCGACaa                   >  2:659504/1‑132 (MQ=255)                                                                                                                   gCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTg           >  1:793953/1‑140 (MQ=255)                                                                                                                   gCTATGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTg           >  1:159034/1‑140 (MQ=255)                                                                                                                      aTGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGaaa        >  1:408913/1‑140 (MQ=255)                                                                                                                      aTGGTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGaaa        >  1:487327/1‑140 (MQ=255)                                                                                                                        ggTTTTTGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGaaaaa      >  2:1389109/1‑140 (MQ=255)                                                                                                                          tttttGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGAAAAAGt    <  1:774184/140‑1 (MQ=255)                                                                                                                            tttGCATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGAAAAAGTCa  <  1:77714/140‑1 (MQ=255)                                                                                                                               |                                                                                                                                         CATGTCACGTTGGGCTTTTTTTGCGAAATCAGTGGGAACCTGGAATAAAAGCAGTTGCCGCAGTTAATTTTCTGCGCTTAGATGTTAATGAATTTAACCCATACCAGTACAATGGCTATGGTTTTTACATTTTACGCAAGGGGCAATTGTGAAACTGGATGAAATCGCTCGGCTGGCGGGAGTGTCGCGGACCACTGCAAGCTATGTTATTAACGGCAAAGCGAAGCAATACCGTGTGAGCGACAAAACCGTTGAAAAAGTCA  >  NC_000913/87880‑88142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑