Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,378,777	(C)6→7	coding (483/1671 nt)	menD ←	2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase, SEPHCHC synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,378,771	1	.	C	100.0%	168.2 / NA	48	G163G (GGA→GGG)	menD	2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase, SEPHCHC synthase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (24/24);  total (24/24)

TTTCCAGACGAGGCGCTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑CCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACATTCCCGGCTGGCGAA  >  NC_000913/2378638‑2378901                                                                                                                                       |                                                                                                                                   tttCCAGACGAGGCGCTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑ccccc                                                                                                                               <  1:595359/139‑1 (MQ=255)             gcgcTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAGCGGGCAGTTGATATGGACT‑cccccccgc                                                                                                                           <  2:73141/131‑4 (MQ=255)             gcgcTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAGCGGGCAGTTGATATGGACT‑cccccccgc                                                                                                                           >  1:73141/1‑128 (MQ=255)             gcgcTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCg                                                                                                                    >  2:986156/1‑139 (MQ=255)                        aGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCg                                                                                                         >  2:352852/1‑139 (MQ=255)                               gTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGa                                                                                                  >  1:570532/1‑139 (MQ=255)                                tttGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccccc                                                                                                                              >  2:530078/1‑109 (MQ=255)                                tttGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccccc                                                                                                                              <  1:530078/109‑1 (MQ=255)                                  tGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATgg                                                                                               >  1:670243/1‑139 (MQ=255)                                        ccTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCg                                                                                                                    >  1:997056/1‑112 (MQ=255)                                        ccTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCg                                                                                                                    <  2:997056/112‑1 (MQ=255)                                          tGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     <  1:1034408/125‑1 (MQ=255)                                          tGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     >  2:1034408/1‑125 (MQ=255)                                          tGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAAcc                                                                                       <  1:986156/139‑1 (MQ=255)                                               ccaGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCa                                                                                  <  2:1453081/139‑1 (MQ=255)                                               ccaGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCa                                                                                  <  2:1197890/139‑1 (MQ=255)                                                    cACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTg                                                                             <  1:556386/139‑1 (MQ=255)                                                      cccAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCg                                                                           >  2:995996/1‑139 (MQ=255)                                                         aGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  1:352852/139‑1 (MQ=255)                                                         aGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  2:670243/139‑1 (MQ=255)                                                         aGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  2:570532/139‑1 (MQ=255)                                                             gCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     <  1:1130272/106‑1 (MQ=255)                                                             gCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     >  2:1130272/1‑106 (MQ=255)                                                                 ttGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCg                                                                                                         >  1:26355/1‑98 (MQ=255)                                                                 ttGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCg                                                                                                         <  2:26355/98‑1 (MQ=255)                                                                         tAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGgc                                                        >  1:1022546/1‑139 (MQ=255)                                                                         tAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccc                                                                                                                                <  2:943857/66‑1 (MQ=255)                                                                         tAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccc                                                                                                                                >  1:943857/1‑66 (MQ=255)                                                                                 gTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCgg                                                    <  2:378454/135‑1 (MQ=255)                                                                                 gTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCgg                                                    >  1:378454/1‑135 (MQ=255)                                                                                  tATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCgaga                                                                                                            <  1:1626403/78‑1 (MQ=255)                                                                                  tATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCgaga                                                                                                            >  2:1626403/1‑78 (MQ=255)                                                                                       tCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  1:1474762/109‑1 (MQ=255)                                                                                       tCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        >  2:1474762/1‑109 (MQ=255)                                                                                       tCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccccccgcat                                                                                                                         <  1:1503601/59‑6 (MQ=255)                                                                                       tCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑cccccccgcat                                                                                                                         >  2:1503601/1‑54 (MQ=255)                                                                                                ccATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCgg                                                    >  1:375491/1‑120 (MQ=255)                                                                                                ccATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCgg                                                    <  2:375491/120‑1 (MQ=255)                                                                                                ccATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTg                                 >  1:161013/1‑139 (MQ=255)                                                                                                    aCAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGt                                                                                              <  2:1325459/74‑1 (MQ=255)                                                                                                    aCAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGt                                                                                              >  1:1325459/1‑74 (MQ=255)                                                                                                    aCAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGt                             <  2:161013/139‑1 (MQ=255)                                                                                                    aCAGCGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGt                             <  2:1277211/139‑1 (MQ=255)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGa                                                                                                                        <  2:1293866/44‑1 (MQ=38)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGa                                                                                                                        >  1:1293866/1‑44 (MQ=255)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGGAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        >  2:1307897/1‑92 (MQ=255)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGGAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  1:1307897/92‑1 (MQ=255)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTc                                                                                                    >  2:498557/1‑64 (MQ=255)                                                                                                        cGGTTCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTc                                                                                                    <  1:498557/64‑1 (MQ=255)                                                                                                           ttCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        <  1:901592/89‑1 (MQ=255)                                                                                                           ttCAGCAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCgggg                                                                        >  2:901592/1‑89 (MQ=255)                                                                                                                cAAACGGGCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACa                 >  1:340103/1‑139 (MQ=255)                                                                                                                     gggCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     <  2:907121/50‑1 (MQ=255)                                                                                                                     gggCAGTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGt                                                                                                     >  1:907121/1‑50 (MQ=255)                                                                                                                          gTTGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACATTCCCGGCTg       >  1:693999/1‑139 (MQ=255)                                                                                                                           ttGATATGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACATTCCCGGCTgg      >  2:715617/1‑139 (MQ=255)                                                                                                                               tatGGACTCCCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACATTCCCGGCTGGCGaa  <  1:715617/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                   TTTCCAGACGAGGCGCTTCACGCAGCCACGGTTTGTCGTCCTGCCACCAGTCACCCAGACGCTGTTGCCAGCTAAGCCCGGTATCGTCCATTTCGCCATACAGCGGTTCAGCAAACGGGCAGTTGATATGGACT‑CCCCCCGCATGAAGCGTACCGAGAGCGTGGTCGATGGTAGAAACCAGCCAACGTGCGGGGATATCCTGGGTCGGGCGCGGCAATGAAATACTGTGCGTGGGGTGAGAGGCGAACATTCCCGGCTGGCGAA  >  NC_000913/2378638‑2378901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑