Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,360,769	G→A	intergenic (+153/‑407)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,360,769	0	G	A	100.0%	186.8 / NA	57	intergenic (+153/‑407)	gltD/gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/30);  total (27/30)

GTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATA  >  NC_000913/3360646‑3360896                                                                                                                            |                                                                                                                                gtCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCaa                                                                                                                  >  1:883101/1‑139 (MQ=255)          aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         <  2:369356/139‑1 (MQ=255)          aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         >  1:1150139/1‑139 (MQ=255)                              cgcgTTGTTTTCTGGCAGATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTATGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                     >  1:924231/1‑139 (MQ=255)                                    gttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTa                                                                                   >  1:574379/1‑135 (MQ=255)                                    gttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTa                                                                                   <  2:574379/135‑1 (MQ=255)                                        tCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAACCCGTCTCAATTACTTGTTaa                                                                           <  2:1150139/139‑1 (MQ=255)                                             cAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                      <  1:1341519/139‑1 (MQ=255)                                               aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATACTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATCTCTCCTTTACAATcc                                                                                             <  1:1079782/114‑1 (MQ=255)                                               aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                             >  2:1079782/1‑114 (MQ=255)                                                                tGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAATCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                           >  2:437191/1‑115 (MQ=255)                                                                tGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAATCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                           <  1:437191/115‑1 (MQ=255)                                                                  aCCTTTCCTATAATATGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                 <  1:673596/139‑1 (MQ=255)                                                                   ccTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAg                                                <  1:134096/139‑1 (MQ=255)                                                                       tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAt                                            >  2:914806/1‑139 (MQ=255)                                                                        ccTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAtt                                           <  2:883101/139‑1 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         >  2:567057/1‑68 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         <  1:567057/68‑1 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                       >  1:99822/1‑102 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                       <  2:99822/102‑1 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCtttt                                  >  2:1082026/1‑139 (MQ=255)                                                                                 gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCtttt                                  >  1:1111760/1‑139 (MQ=255)                                                                                 gggATAATTTTCAACAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCtttt                                  >  1:1602127/1‑139 (MQ=255)                                                                                  ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                                 >  2:358416/1‑139 (MQ=255)                                                                                    aTACTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATACGTCTCAATTACTTGTTCACACct                                                                      >  1:1036379/1‑100 (MQ=255)                                                                                    aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                      <  2:1036379/100‑1 (MQ=255)                                                                                     tAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAtt                              <  2:924231/139‑1 (MQ=255)                                                                                           tCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                           >  2:403920/1‑88 (MQ=255)                                                                                           tCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                           <  1:403920/88‑1 (MQ=255)                                                                                           tCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                 >  1:355446/1‑114 (MQ=255)                                                                                           tCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                 <  2:355446/114‑1 (MQ=255)                                                                                            cAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                      <  2:1294910/92‑1 (MQ=255)                                                                                            cAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                      >  1:1294910/1‑92 (MQ=255)                                                                                              aTAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTaaa                     <  1:914806/139‑1 (MQ=255)                                                                                                  aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         >  2:641622/1‑51 (MQ=255)                                                                                                  aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                         <  1:641622/51‑1 (MQ=255)                                                                                                  aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGt                 <  1:358416/139‑1 (MQ=255)                                                                                                      tgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctc                                                                     <  2:1158082/83‑1 (MQ=255)                                                                                                      tgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctc                                                                     >  1:1158082/1‑83 (MQ=255)                                                                                                       gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa            <  2:1561924/139‑1 (MQ=255)                                                                                                       gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa            <  2:18302/139‑1 (MQ=255)                                                                                                           tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                             <  1:591849/118‑1 (MQ=255)                                                                                                           tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                             >  2:591849/1‑118 (MQ=255)                                                                                                           tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATACTGCAAGCTATTCAg                                        <  2:59016/107‑1 (MQ=255)                                                                                                           tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATACTGCAAGCTATTCAg                                        >  1:59016/1‑107 (MQ=255)                                                                                                             ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACaa                                                                                                >  1:1470300/1‑49 (MQ=255)                                                                                                             ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACaa                                                                                                <  2:1470300/49‑1 (MQ=255)                                                                                                               cACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAata    <  1:1082026/139‑1 (MQ=255)                                                                                                                aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAatat   >  2:20991/1‑139 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAAt                                                                                               <  2:377079/42‑1 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAAt                                                                                               >  1:377079/1‑42 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTa                                                                            <  2:578393/61‑1 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTa                                                                            >  1:578393/1‑61 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCa                                         >  2:408581/1‑96 (MQ=255)                                                                                                                     gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCa                                         <  1:408581/96‑1 (MQ=255)                                                                                                                       cTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAAtata  <  2:271470/133‑1 (MQ=255)                                                                                                                       cTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAAtata  >  1:271470/1‑133 (MQ=255)                                                                                                                            |                                                                                                                                GTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATA  >  NC_000913/3360646‑3360896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑