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%	207.6 / NA	63	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 (29/34);  total (29/34)

CAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAAT  >  NC_000913/3360638‑3360902                                                                                                                                    |                                                                                                                                      cAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAg                                                                                                                                <  2:1236740/139‑1 (MQ=255)        tgtCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCa                                                                                                                         >  1:819900/1‑139 (MQ=255)              gCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                                   >  1:404197/1‑139 (MQ=255)                gAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAttt                                                                                                                 <  2:248535/139‑1 (MQ=255)                  aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGTGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               <  1:3693/139‑1 (MQ=255)                  aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               <  2:589332/139‑1 (MQ=255)                  aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               >  1:1297330/1‑139 (MQ=255)                  aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               >  2:321269/1‑139 (MQ=255)                           cTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACaa                                                                                                      <  1:204199/139‑1 (MQ=255)                              aCGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                                   <  2:457804/139‑1 (MQ=255)                                   gTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               <  1:1153102/122‑1 (MQ=255)                                   gTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATAAAGCAATTtct                                                                                                               >  2:1153102/1‑122 (MQ=255)                                      cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                           >  2:1164590/1‑139 (MQ=255)                                        cgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCATTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTa                                                                                         >  2:371907/1‑139 (MQ=255)                                         gttgttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTAc                                                                                        <  2:819900/139‑1 (MQ=255)                                          ttgttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACt                                                                                       >  2:795618/1‑139 (MQ=255)                                                       aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctct                                                                          <  1:795618/139‑1 (MQ=255)                                                       aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctct                                                                          >  1:1171894/1‑139 (MQ=255)                                                            ggCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACaa                                                                     >  1:1045720/1‑139 (MQ=255)                                                                      tttGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                             >  1:629970/1‑121 (MQ=255)                                                                      tttGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                             <  2:629970/121‑1 (MQ=255)                                                                         gACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                        <  2:404197/139‑1 (MQ=255)                                                                           ccTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCATTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAg                                                      <  1:371907/139‑1 (MQ=255)                                                                               tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAt                                                  <  1:321269/139‑1 (MQ=255)                                                                                   ataataGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                              <  2:1045720/139‑1 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               <  2:59402/67‑1 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               >  1:59402/1‑67 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                                 <  2:70475/97‑1 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                                 >  1:70475/1‑97 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                              <  1:953899/132‑1 (MQ=255)                                                                                          ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                              >  2:953899/1‑132 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               <  1:1058365/66‑1 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                               >  2:1058365/1‑66 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGAc                                                                       >  1:194443/1‑106 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGAc                                                                       <  2:194443/106‑1 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAtt                                                 >  1:907627/1‑128 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAtt                                                 <  2:907627/128‑1 (MQ=255)                                                                                           gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCa                                      >  2:1022841/1‑139 (MQ=255)                                                                                            aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTTTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                                >  1:355668/1‑128 (MQ=255)                                                                                            aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                             <  1:1125028/99‑1 (MQ=255)                                                                                            aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                             >  2:1125028/1‑99 (MQ=255)                                                                                            aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                                <  2:355668/128‑1 (MQ=255)                                                                                              aaTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                                   >  2:675550/1‑75 (MQ=255)                                                                                              aaTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                                   <  1:675550/75‑1 (MQ=255)                                                                                              aaTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                                   <  2:3923/139‑1 (MQ=255)                                                                                                          aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCAt                                >  2:294385/1‑130 (MQ=255)                                                                                                          aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCAt                                <  1:294385/130‑1 (MQ=255)                                                                                                            tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAaca                                                                               >  1:50220/1‑81 (MQ=255)                                                                                                            tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAaca                                                                               <  2:50220/81‑1 (MQ=255)                                                                                                            tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct                     <  2:1297330/139‑1 (MQ=255)                                                                                                            tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct                     <  1:1022841/139‑1 (MQ=255)                                                                                                               gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa                  <  2:1171894/139‑1 (MQ=255)                                                                                                                     ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTaa            >  1:995055/1‑139 (MQ=255)                                                                                                                     ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTaa            <  2:995055/139‑1 (MQ=255)                                                                                                                        aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                        <  2:382341/92‑1 (MQ=255)                                                                                                                        aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                        >  1:382341/1‑92 (MQ=255)                                                                                                                        aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa                  <  1:270382/130‑1 (MQ=255)                                                                                                                        aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa                  >  2:270382/1‑130 (MQ=255)                                                                                                                             gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                        <  1:988141/87‑1 (MQ=255)                                                                                                                             gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                        >  2:988141/1‑87 (MQ=255)                                                                                                                             gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCg                   <  2:1115036/124‑1 (MQ=255)                                                                                                                             gTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCg                   >  1:1115036/1‑124 (MQ=255)                                                                                                                               cTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAat  >  1:1127281/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                      CAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAAT  >  NC_000913/3360638‑3360902

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: ‑