Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,979,943	C→T	A308V (GCT→GTT)  *231* (TAG→TAA)	lysR → ygeA ←	transcriptional activator of lysA, autorepressor Asp/Glu_racemase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,979,943	0	C	T	100.0%	209.0 / NA	64	A308V (GCT→GTT)  *231* (TAG→TAA)	lysR ygeA	transcriptional activator of lysA, autorepressor Asp/Glu_racemase family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (34/30);  total (34/30)

GCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGCTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTC  >  NC_000913/2979810‑2980077                                                                                                                                      |                                                                                                                                       gCGGTTCGGTTCACGGTCAGCCTGATCCGCCCCCTGCACCGCCCATCATCAGCGCTGGTTCAGGGTTTTGGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  1:192971/139‑1 (MQ=255) gCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  2:923761/139‑1 (MQ=255) gCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  1:1835543/139‑1 (MQ=255) gCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  2:200636/139‑1 (MQ=255)       ccGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCAt                                                                                                                             >  2:192971/1‑139 (MQ=255)          ttCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATaaa                                                                                                                          >  2:460838/1‑139 (MQ=255)             aCCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACg                                                                                                                                    <  1:265779/126‑1 (MQ=255)             aCCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACg                                                                                                                                    >  2:265779/1‑126 (MQ=255)                  cAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAg                                                                                                                  >  1:1550700/1‑139 (MQ=255)                    gCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCa                                                                                                                >  2:186297/1‑139 (MQ=255)                         aTCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATcc                                                                                                             <  1:1389643/137‑1 (MQ=255)                         aTCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATcc                                                                                                             >  2:1389643/1‑137 (MQ=255)                                  cTGCACCGCCCCTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGAt                                                                                                  <  2:1219028/139‑1 (MQ=255)                                   tGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATc                                                                                                 >  2:1298179/1‑139 (MQ=255)                                             gTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTAt                                                                                       <  1:186297/139‑1 (MQ=255)                                               catcaGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCa                                                                                     >  1:1649639/1‑139 (MQ=255)                                                       cTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   >  2:218357/1‑85 (MQ=255)                                                       cTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  1:218357/85‑1 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                >  2:1217293/1‑117 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                <  1:1217293/117‑1 (MQ=255)                                                                            cATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACa                                                                                                                   <  2:1761710/80‑1 (MQ=255)                                                                            cATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACa                                                                                                                   >  1:1761710/1‑80 (MQ=255)                                                                                tACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCAcc                                                    >  2:14338/1‑139 (MQ=255)                                                                                    aGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAATGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTa                                                >  1:1280779/1‑139 (MQ=255)                                                                                    aGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGc                                                                                                                 <  1:370811/74‑1 (MQ=255)                                                                                    aGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGc                                                                                                                 >  2:370811/1‑74 (MQ=255)                                                                                    aGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTa                                                >  1:1718447/1‑139 (MQ=255)                                                                                       ggggTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAAc                                             <  1:460838/139‑1 (MQ=255)                                                                                        gggTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAAcc                                            >  2:1679772/1‑139 (MQ=255)                                                                                             aCCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTAc                                                                                                                                     >  2:481851/1‑45 (MQ=255)                                                                                             aCCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTAc                                                                                                                                     <  1:481851/45‑1 (MQ=255)                                                                                             aCCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGc                                                                                                                 <  1:300271/65‑1 (MQ=255)                                                                                             aCCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGc                                                                                                                 >  2:300271/1‑65 (MQ=255)                                                                                                  aaCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCtgtg                                  <  1:14338/139‑1 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   >  1:221690/1‑41 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  2:221690/41‑1 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGc                                 >  1:446817/1‑139 (MQ=255)                                                                                                       gTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                <  2:129098/88‑1 (MQ=255)                                                                                                       gTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                >  1:129098/1‑88 (MQ=255)                                                                                                       gTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGcc                             >  2:1204223/1‑139 (MQ=255)                                                                                                        tCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   >  1:1125023/1‑36 (MQ=255)                                                                                                        tCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                   <  2:1125023/36‑1 (MQ=255)                                                                                                        tCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             <  2:1677742/74‑1 (MQ=255)                                                                                                        tCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             >  1:1677742/1‑74 (MQ=255)                                                                                                         cACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCaa                           <  1:1298179/139‑1 (MQ=255)                                                                                                          aCTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCaaa                          >  2:1453635/1‑139 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATg                                                                                                     >  1:1712753/1‑57 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATg                                                                                                     <  2:1712753/57‑1 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             <  1:366163/65‑1 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             >  2:366163/1‑65 (MQ=255)                                                                                                                  tGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGc                  <  2:1743865/139‑1 (MQ=255)                                                                                                                    aCGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATGCTCGGCATGGATCGCcgcg                                                                                           >  1:1332685/1‑64 (MQ=255)                                                                                                                    aCGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCcgcg                                                                                           <  2:1332685/64‑1 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             <  1:453707/60‑1 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             >  2:453707/1‑60 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAac                                                                                  >  1:887724/1‑71 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAac                                                                                  <  2:887724/71‑1 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCtg              >  1:864151/1‑139 (MQ=255)                                                                                                                          ttttGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTgcg          <  2:1280779/139‑1 (MQ=255)                                                                                                                           tttGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCtgtg                                  <  1:790242/114‑1 (MQ=255)                                                                                                                           tttGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCtgtg                                  >  2:790242/1‑114 (MQ=255)                                                                                                                               tcgtcAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             <  2:237478/51‑1 (MQ=255)                                                                                                                               tcgtcAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                             >  1:237478/1‑51 (MQ=255)                                                                                                                                  tcAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTc  >  2:1791107/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                       GCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGCTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTC  >  NC_000913/2979810‑2980077

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: ‑