Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	85,430	G→A	A306T (GCA→ACA)	cra →	catabolite repressor/activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	85,430	0	G	A	100.0%	223.3 / NA	59	A306T (GCA→ACA)	cra	catabolite repressor/activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/28);  total (31/28)

GGCAAACTGCCTTCTGACCTGGCAATTGCCACCTTTGGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTA  >  NZ_CP009273/85298‑85565                                                                                                                                     |                                                                                                                                        ggCAAACTGCCTTCTGACCTGGCAATTGCCACCTTTGGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGcc                                                                                                                                   <  2:382146/139‑1 (MQ=255)                    tGGCAATTGCCACCTTTGGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGc                                                                                                                 >  2:8783/1‑138 (MQ=255)                                    tGGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAAcg                                                                                                >  1:934518/1‑139 (MQ=255)                                              gAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAAc                                                                                      <  1:1003050/139‑1 (MQ=255)                                                 cTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTa                                                                                   <  1:8783/139‑1 (MQ=255)                                                 cTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTa                                                                                   <  1:567645/139‑1 (MQ=255)                                                    cTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAAtc                                                                                >  2:781228/1‑139 (MQ=255)                                                    cTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAAtc                                                                                >  1:252315/1‑139 (MQ=255)                                                    cTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAAtc                                                                                >  1:849445/1‑139 (MQ=255)                                                            cttACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATcgc                                                                        >  2:846638/1‑139 (MQ=255)                                                                  gtgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATcgcc                                                                       <  2:1275591/134‑1 (MQ=255)                                                                  gtgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATcgcc                                                                       >  1:1275591/1‑134 (MQ=255)                                                                   tgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCgcggcg                                                                 >  2:979664/1‑139 (MQ=255)                                                                   tgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCgcggcg                                                                 >  2:455127/1‑139 (MQ=255)                                                                   tgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCgcggcg                                                                 >  1:780934/1‑139 (MQ=255)                                                                   tgtCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCgcggcg                                                                 >  1:324198/1‑139 (MQ=255)                                                                     tCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGt                                                                                                                     >  1:787950/1‑85 (MQ=255)                                                                     tCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGt                                                                                                                     <  2:787950/85‑1 (MQ=255)                                                                     tCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTg                                                               >  2:1165566/1‑139 (MQ=255)                                                                     tCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTg                                                               >  1:649788/1‑139 (MQ=255)                                                                     tCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTg                                                               >  1:383449/1‑139 (MQ=255)                                                                      ccGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGc                                                              >  1:1001988/1‑139 (MQ=255)                                                                       cGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCt                                                             >  1:1222021/1‑139 (MQ=255)                                                                       cGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCt                                                             <  1:979664/139‑1 (MQ=255)                                                                       cGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCt                                                             <  1:470725/139‑1 (MQ=255)                                                                       cGGTGCTGGCAGTGGCACAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCt                                                             <  1:595005/139‑1 (MQ=255)                                                                            cTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGc                                                         <  1:455127/138‑1 (MQ=255)                                                                            cTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCGGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGc                                                         <  2:1138685/138‑1 (MQ=255)                                                                              ggCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCg                                                       >  2:743771/1‑138 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGcc                                                                                                                                   >  1:266416/1‑61 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGcc                                                                                                                                   <  2:266416/61‑1 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCg                                                       >  2:96429/1‑137 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCg                                                       >  2:752253/1‑137 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCg                                                       <  1:1165566/137‑1 (MQ=255)                                                                               gCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCg                                                       >  2:1068574/1‑137 (MQ=255)                                                                                  gTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCt                                                  <  1:752253/139‑1 (MQ=255)                                                                                                              agCGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGt                      >  2:1244115/1‑139 (MQ=255)                                                                                                                cGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAAt                                                                                 >  1:1229039/1‑78 (MQ=255)                                                                                                                cGTGTGCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAAt                                                                                 <  2:1229039/78‑1 (MQ=255)                                                                                                                  tgtgCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAAt                  >  2:832827/1‑139 (MQ=255)                                                                                                                  tgtgCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAAt                  >  2:633930/1‑139 (MQ=255)                                                                                                                    tgCTGGAGATTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAAttt                >  2:458125/1‑139 (MQ=255)                                                                                                                         gagaTTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCct            <  2:649788/138‑1 (MQ=255)                                                                                                                          agaTTGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCctct          >  1:99095/1‑139 (MQ=255)                                                                                                                              tGTCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGgcg      >  2:330884/1‑139 (MQ=255)                                                                                                                                tCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAAttt                <  2:776044/127‑1 (MQ=255)                                                                                                                                tCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAAttt                >  1:776044/1‑127 (MQ=255)                                                                                                                                tCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGcgcg    <  2:324198/139‑1 (MQ=255)                                                                                                                                tCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGcgcg    >  2:542198/1‑139 (MQ=255)                                                                                                                                tCCTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGcgcg    <  2:849445/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:743771/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:1008485/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:1057747/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:542198/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:1144924/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:832827/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:853962/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:922304/139‑1 (MQ=255)                                                                                                                                  cTGACAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTa  <  1:1244115/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                        GGCAAACTGCCTTCTGACCTGGCAATTGCCACCTTTGGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTA  >  NZ_CP009273/85298‑85565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑