Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,417	A→G	intergenic (+40/+22)	rhtC → / ← rhtB	L‑threonine exporter/L‑homoserine/L‑homoserine lactone/L‑threonine exporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,417	0	A	G	100.0%	190.3 / NA	52	intergenic (+40/+22)	rhtC/rhtB	L‑threonine exporter/L‑homoserine/L‑homoserine lactone/L‑threonine exporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/25);  total (27/25)

GCCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTACGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGT  >  NC_000913/4008286‑4008550                                                                                                                                    |                                                                                                                                      gcCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCAt                                                                                                                               >  1:520794/1‑140 (MQ=255)  ccGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATc                                                                                                                              >  2:764458/1‑140 (MQ=255)  ccGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATc                                                                                                                              >  1:73144/1‑140 (MQ=255)     tGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGa                                                                                                                           >  2:556316/1‑140 (MQ=255)              aCGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTAtttt                                                                                                                  <  1:924530/140‑1 (MQ=255)                 tCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCa                                                                                                               >  1:842248/1‑140 (MQ=255)                 tCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCa                                                                                                               >  2:614528/1‑140 (MQ=255)                  cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCa                                                                                                                                <  2:866606/122‑1 (MQ=255)                  cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCa                                                                                                                                >  1:866606/1‑122 (MQ=255)                  cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTACCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCAc                                                                                                              >  2:316481/1‑140 (MQ=255)                   tGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACg                                                                                                             <  1:556316/140‑1 (MQ=255)                   tGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACg                                                                                                             <  2:950982/140‑1 (MQ=255)                     gCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCa                                                                                                           <  1:614528/140‑1 (MQ=255)                          gTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCt                                                                                                      >  2:945563/1‑140 (MQ=255)                            ggATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCg                                                                                                    <  2:1123807/140‑1 (MQ=255)                              aTTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGcc                                                                                                  <  2:851942/140‑1 (MQ=255)                                   tGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGc                                                                                             >  2:260217/1‑140 (MQ=255)                                       tttGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAAc                                                                                         >  1:818057/1‑140 (MQ=255)                                        ttGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACa                                                                                        <  2:830231/140‑1 (MQ=255)                                             ggggCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCt                                                                                   <  2:54363/140‑1 (MQ=255)                                                 cGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               <  1:688721/140‑1 (MQ=255)                                                     aTTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAg                                                                           >  2:887055/1‑140 (MQ=255)                                                        tGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCAt                                                                        >  2:970553/1‑140 (MQ=255)                                                         gCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATa                                                                       <  1:37149/140‑1 (MQ=255)                                                              aTTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               >  1:372037/1‑127 (MQ=255)                                                              aTTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               <  2:372037/127‑1 (MQ=255)                                                                    cattcattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGcc                                                            <  2:818057/140‑1 (MQ=255)                                                                      ttcattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGa                                                          <  1:964462/140‑1 (MQ=255)                                                                        cattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGaaa                                                        >  1:941107/1‑140 (MQ=255)                                                                          tttGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAAt                                                      >  1:41164/1‑140 (MQ=255)                                                                                   ttCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAg                                             >  2:1110665/1‑140 (MQ=255)                                                                                       cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         >  2:571879/1‑140 (MQ=255)                                                                                       cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         <  1:970553/140‑1 (MQ=255)                                                                                       cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         >  1:861389/1‑140 (MQ=255)                                                                                        ggTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCt                                        >  2:520753/1‑140 (MQ=255)                                                                                        ggTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCt                                        >  2:117053/1‑140 (MQ=255)                                                                                            aTGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCAt                                    >  1:46782/1‑140 (MQ=255)                                                                                                     gcgTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  2:491308/140‑1 (MQ=255)                                                                                                     gcgTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  1:571879/140‑1 (MQ=255)                                                                                                        tCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTcc                        >  1:730896/1‑140 (MQ=255)                                                                                                            cAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTa                    <  2:73144/140‑1 (MQ=255)                                                                                                            cAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAACAGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTa                    <  1:632325/140‑1 (MQ=255)                                                                                                                 tAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCa               <  1:117053/140‑1 (MQ=255)                                                                                                                   aGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATa             >  2:242419/1‑140 (MQ=255)                                                                                                                   aGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATa             >  1:1124737/1‑140 (MQ=255)                                                                                                                     tCGGGTAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           >  2:523260/1‑124 (MQ=255)                                                                                                                     tCGGGTAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  1:523260/124‑1 (MQ=255)                                                                                                                        gATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCa        <  1:242419/140‑1 (MQ=255)                                                                                                                        gATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCa        <  1:945563/140‑1 (MQ=255)                                                                                                                          tAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCCCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAAt      <  1:113100/140‑1 (MQ=255)                                                                                                                             ggCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCg   <  2:520794/140‑1 (MQ=255)                                                                                                                              gCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGt  <  1:260217/140‑1 (MQ=255)                                                                                                                              gCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGt  >  2:226709/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                      GCCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTACGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGT  >  NC_000913/4008286‑4008550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑