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%	132.4 / NA	41	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 (18/23);  total (18/23)

GCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAATAT  >  NC_000913/3360636‑3360904                                                                                                                                      |                                                                                                                                        gCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGa                                                                                                                                    <  1:43525/139‑1 (MQ=255)   cAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAg                                                                                                                                  <  2:18362/139‑1 (MQ=255)                    aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                                 >  2:255723/1‑139 (MQ=255)                    aTCAAATTACTGACGAAGCGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                                 >  1:252965/1‑139 (MQ=255)                                        cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                             >  2:759215/1‑139 (MQ=255)                                                  tCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                                   <  1:713777/139‑1 (MQ=255)                                                    tGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAaca                                                                                 <  1:759215/139‑1 (MQ=255)                                                                            aCCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                         <  2:825208/139‑1 (MQ=255)                                                                            aCCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                         <  1:255723/139‑1 (MQ=255)                                                                                ttCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTa                                                     >  2:390243/1‑139 (MQ=255)                                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                         >  2:285146/1‑134 (MQ=255)                                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCaa                                                         <  1:285146/134‑1 (MQ=255)                                                                                            ggATACTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtctc                                                                                                                <  1:497956/68‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAttt                                                                                                                   <  2:174753/65‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAttt                                                                                                                   >  1:174753/1‑65 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtctc                                                                                                                >  2:497956/1‑68 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACaa                                                                                                        >  1:638736/1‑76 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAAt                                                                                                       >  1:127249/1‑77 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAAt                                                                                                       <  2:127249/77‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                                >  1:616175/1‑132 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                                <  2:616175/132‑1 (MQ=255)                                                                                            ggATAATTTTCAATAAATTGTGCTTGGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACaa                                                                                                        <  2:638736/76‑1 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCg                                                                                                    >  1:34128/1‑79 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCg                                                                                                    <  2:34128/79‑1 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                                  >  1:376769/1‑129 (MQ=255)                                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                                  <  2:376769/129‑1 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGcaca                                                                                                                              <  1:297970/52‑1 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGcaca                                                                                                                              >  2:297970/1‑52 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                                   >  1:639360/1‑95 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                                   <  2:639360/95‑1 (MQ=255)                                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAt                                       <  1:812386/139‑1 (MQ=255)                                                                                               tAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAtt                                      <  2:117473/139‑1 (MQ=255)                                                                                                 aTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                                >  2:256534/1‑127 (MQ=255)                                                                                                 aTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                                <  1:256534/127‑1 (MQ=255)                                                                                                       aaTAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTaa                              >  1:31349/1‑139 (MQ=255)                                                                                                                tgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                                 >  2:133208/1‑47 (MQ=255)                                                                                                                tgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                                 <  1:133208/47‑1 (MQ=255)                                                                                                                    ttGTTCACCATGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGatat                 <  2:252965/139‑1 (MQ=255)                                                                                                                     tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                               <  2:25679/76‑1 (MQ=255)                                                                                                                     tGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                               >  1:25679/1‑76 (MQ=255)                                                                                                                      gTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTa               <  2:31349/139‑1 (MQ=255)                                                                                                                                   gataaGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCACTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAatat  <  2:600676/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                        GCCAGACTGTGTCTGGCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATATACAAAATAT  >  NC_000913/3360636‑3360904

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: ‑