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%	121.8 / NA	38	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 (15/23);  total (15/23)

GCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTA  >  NC_000913/3360636‑3360891                                                                                                                                      |                                                                                                                           gCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGa                                                                                                                       <  2:691221/139‑1 (MQ=255)     gACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGc                                                                                                                    <  2:240331/138‑1 (MQ=255)     gACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGc                                                                                                                    >  1:240331/1‑138 (MQ=255)                               gACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATc                                                                                         >  2:16232/1‑139 (MQ=255)                                        cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                <  2:364297/139‑1 (MQ=255)                                          cgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTa                                                                              <  2:183462/139‑1 (MQ=255)                                           gttgttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTAc                                                                             <  2:661202/139‑1 (MQ=255)                                           gttgttTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTAc                                                                             <  1:719305/139‑1 (MQ=255)                                                         aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctct                                                               >  1:68173/1‑139 (MQ=255)                                                            gCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGAc                                                            <  2:276069/139‑1 (MQ=255)                                                                    aGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGa                                                    <  1:570052/139‑1 (MQ=255)                                                                        tttGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCt                                                <  1:362771/139‑1 (MQ=255)                                                                          tGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGc                                              <  1:651003/139‑1 (MQ=255)                                                                                ttCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTa                                        >  1:740245/1‑139 (MQ=255)                                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAt                                       <  2:68173/139‑1 (MQ=255)                                                                                           gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCtttt                             >  2:783877/1‑139 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGTACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                <  2:509345/87‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGTACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                >  1:509345/1‑87 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctc                                                                <  1:737722/103‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctc                                                                >  2:737722/1‑103 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                            >  2:675387/1‑139 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                            >  2:788718/1‑139 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                            >  1:675751/1‑139 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                            >  1:193057/1‑139 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCa                                    >  2:526126/1‑130 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCa                                    <  1:526126/130‑1 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAt                          >  2:175901/1‑139 (MQ=255)                                                                                                            aTTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGt            >  1:628096/1‑139 (MQ=255)                                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct          <  1:71416/139‑1 (MQ=255)                                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct          <  2:599029/139‑1 (MQ=255)                                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct          <  2:628096/139‑1 (MQ=255)                                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct          <  1:220146/139‑1 (MQ=255)                                                                                                              tgtgCTTTGTTCAACAAGTCTGATAATTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct          <  2:765490/139‑1 (MQ=255)                                                                                                                 gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa       <  1:783877/139‑1 (MQ=255)                                                                                                                 gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa       <  1:675387/139‑1 (MQ=255)                                                                                                                      gTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTa  <  1:16232/139‑1 (MQ=255)                                                                                                                          aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                  >  2:592601/1‑71 (MQ=255)                                                                                                                          aCCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                  <  1:592601/71‑1 (MQ=255)                                                                                                                                      |                                                                                                                           GCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTA  >  NC_000913/3360636‑3360891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑