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%	174.4 / NA	54	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 (29/25);  total (29/25)

GCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGCTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTCT  >  NC_000913/2979810‑2980078                                                                                                                                      |                                                                                                                                        gCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                    <  2:1570319/139‑1 (MQ=255) gCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGa                                                                                                                                    >  2:1479569/1‑139 (MQ=255)                     ccTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCAt                                                                                                                >  1:902058/1‑139 (MQ=255)                         aTCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTc                                                                                                            >  1:778726/1‑139 (MQ=255)                                    gCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATa                                                                                                                             >  2:516516/1‑111 (MQ=255)                                    gCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATa                                                                                                                             <  1:516516/111‑1 (MQ=255)                                       ccGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATcgccg                                                                                              <  1:812806/139‑1 (MQ=255)                                         gCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATa                                                                                                                             >  1:1306769/1‑106 (MQ=255)                                         gCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATa                                                                                                                             <  2:1306769/106‑1 (MQ=255)                                          cccGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCgg                                                                                           >  2:1346990/1‑139 (MQ=255)                                                  caGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAac                                                                                   <  1:1479569/139‑1 (MQ=255)                                                    gcgcTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                 >  2:20717/1‑139 (MQ=255)                                                    gcgcTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAacac                                                                                 <  1:20717/139‑1 (MQ=255)                                                                gCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACt                                                                     >  2:730697/1‑139 (MQ=255)                                                                    ttAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTgcgc                                                                 >  2:26870/1‑139 (MQ=255)                                                                     tAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGct                                                                <  1:1346990/139‑1 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACTACAGCATAAAAGCGACAGCATCCt                                                                                                             <  1:1132894/89‑1 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGc                                                                                                                                <  1:1622849/70‑1 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGc                                                                                                                                >  2:1622849/1‑70 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCtcttct                                                           >  1:1344479/1‑139 (MQ=255)                                                                          ggCATTTACAAGCGGGGTTAACGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCt                                                                                                             >  2:1132894/1‑89 (MQ=255)                                                                            cATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAg                                                                                                                         <  1:1393510/75‑1 (MQ=255)                                                                            cATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAg                                                                                                                         >  2:1393510/1‑75 (MQ=255)                                                                                   aaGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGt                                                  <  2:1344479/139‑1 (MQ=255)                                                                                             aCCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAAttt                                        <  2:902058/139‑1 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCt                                                                                                             <  2:1669038/64‑1 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCt                                                                                                             >  1:1669038/1‑64 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGct                                                                <  1:571459/109‑1 (MQ=255)                                                                                                   aCTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGct                                                                >  2:571459/1‑109 (MQ=255)                                                                                                       gTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGt                                                  >  1:57893/1‑119 (MQ=255)                                                                                                       gTCACTTCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGt                                                  <  2:57893/119‑1 (MQ=255)                                                                                                            ttCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTgcgc                                                                 <  1:1417193/99‑1 (MQ=255)                                                                                                            ttCTCTTGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTgcgc                                                                 >  2:1417193/1‑99 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACGGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCtctt                                                             <  2:1141581/98‑1 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACGGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCtctt                                                             >  1:1141581/1‑98 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACatcatc                                                                                                               >  2:1118798/1‑48 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCAt                                                                                                                <  2:1141767/47‑1 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCAt                                                                                                                >  1:1141767/1‑47 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATc                                                                                                               <  1:1118798/48‑1 (MQ=255)                                                                                                                 ttGACGCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACg                    >  1:890662/1‑139 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATg                                                                                                      >  1:734538/1‑52 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATg                                                                                                      <  2:734538/52‑1 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTgcg                                                                  <  2:1051456/88‑1 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTgcg                                                                  >  1:1051456/1‑88 (MQ=255)                                                                                                                      gCTATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCtg               >  2:954353/1‑139 (MQ=255)                                                                                                                        tATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGccc                 <  2:1650256/135‑1 (MQ=255)                                                                                                                        tATTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGccc                 >  1:1650256/1‑135 (MQ=255)                                                                                                                         aTTTTGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTgc            >  1:468473/1‑139 (MQ=255)                                                                                                                            ttGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGcc         <  2:890662/139‑1 (MQ=255)                                                                                                                             tGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAaca                                                                       >  1:773318/1‑76 (MQ=255)                                                                                                                             tGTCGTCAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAaca                                                                       <  2:773318/76‑1 (MQ=255)                                                                                                                                  tcAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGct                                                                <  2:1257161/78‑1 (MQ=255)                                                                                                                                  tcAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGct                                                                >  1:1257161/1‑78 (MQ=255)                                                                                                                                   cAGTTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTCt  >  2:646196/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                        GCGGTTCCGTTCACCGTCAGCCTGATCCGCCCCCTGCACCGCCCGTCATCAGCGCTGGTTCAGGCGTTTAGTGGGCATTTACAAGCGGGGTTACCGAAACTGGTCACTTCTCTTGACGCTATTTTGTCGTCAGCTACGACAGCATAAAAGCGACAGCATCCTCGGCATGGATCGCCGCGGTATCAAACACAGGCAAAACACTGCGCTCTTCTGGCACCAGTAAACCAATTTCTGTGCAGCCAAAAATGACGCCCTGTGCGCCCTGTTCT  >  NC_000913/2979810‑2980078

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑