Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,952,569	C→T	A29V (GCG→GTG)	ilvE →	branched‑chain amino acid aminotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,952,569	0	C	T	100.0%	211.8 / NA	62	A29V (GCG→GTG)	ilvE	branched‑chain amino acid aminotransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (33/29);  total (33/29)

AGGAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGCGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCGT  >  NC_000913/3952472‑3952663                                                                                                  |                                                                                               aGGAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACgtgc                                                                                              <  1:643621/100‑1 (MQ=255)  ggAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCt                                                                                             >  2:551517/1‑100 (MQ=255)  ggAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCt                                                                                             >  2:1212911/1‑100 (MQ=255)   gAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGGTGGGAAGAAGCGAAGGTGCATGTGATGTCGCACGTGCt                                                                                             >  1:819213/1‑99 (MQ=255)   gAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTg                                                                                            >  2:204497/1‑100 (MQ=255)    aaTATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGtgctgc                                                                                           >  1:923888/1‑100 (MQ=255)     atatAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCa                                                                                          <  1:204497/100‑1 (MQ=255)      tataAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCAc                                                                                         <  1:1508278/100‑1 (MQ=255)       ataAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACt                                                                                        >  2:1142612/1‑100 (MQ=255)        tgaaaaTGACCACGAAGAAAGCTGATTACATTTGGTTCGATGGCGAGATGGTTCGCTGGGAAGCAGCGACGGTGAATGTGATGTCGCACGTGCTGCAcca                                                                                       >  1:985300/3‑98 (MQ=255)        taAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTa                                                                                       <  1:17319/100‑1 (MQ=255)        taAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTa                                                                                       >  2:383615/1‑100 (MQ=255)        taAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGAGAAGACGCGAACGTGCATGTGATGTCGCATGTGCTGCACt                                                                                        >  1:1234629/1‑99 (MQ=255)          aaaaTGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATg                                                                                     >  1:933509/1‑100 (MQ=255)          aaaaTGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATg                                                                                     <  1:739146/100‑1 (MQ=255)            aaTGACCACGAAGAAAGCTGATTAGATGTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGc                                                                                   <  1:19392/100‑1 (MQ=255)            aaTGACCACGAAGAAAGCTGATTACATTTTGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGc                                                                                   <  1:359589/100‑1 (MQ=255)                 ccACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTc                                                                              >  2:708704/1‑100 (MQ=255)                  cACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCg                                                                             <  2:785764/100‑1 (MQ=255)                    cGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGCTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGt                                                                           <  1:989725/100‑1 (MQ=255)                     gaagaaCGCTGATTATATTTGGTTCAATGGTGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGtt                                                                          <  2:1633083/100‑1 (MQ=255)                      aagaaAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGttt                                                                         <  2:1133953/100‑1 (MQ=255)                        gaaAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGttttt                                                                       >  1:763405/1‑100 (MQ=255)                          aaGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGttttt                                                                       <  1:1708362/98‑1 (MQ=255)                             cTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAgg                                                                  <  2:449971/100‑1 (MQ=255)                             cTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAg                                                                   <  2:1654998/99‑1 (MQ=255)                                   aCATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCg                                                            <  2:742670/100‑1 (MQ=255)                                    cATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGt                                                           >  1:131445/1‑100 (MQ=255)                                         ggTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTa                                                      >  2:223536/1‑100 (MQ=255)                                         ggTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTa                                                      >  1:533139/1‑100 (MQ=255)                                          gTTTAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTAc                                                     <  1:1281299/100‑1 (MQ=255)                                          gTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTAc                                                     >  1:161331/1‑100 (MQ=255)                                            tCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGa                                                   <  2:104052/100‑1 (MQ=255)                                             cAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGTCACTTCGGTTTTTGAAGGCATCCGTTGCTACGAc                                                  >  1:362151/1‑100 (MQ=255)                                                tGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCg                                               >  1:1400642/1‑100 (MQ=255)                                                tGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCg                                               >  2:497614/1‑100 (MQ=255)                                                tGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAAGCATCCGTTGCTACGACTCg                                               >  2:1601705/1‑100 (MQ=255)                                                 ggggAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTc                                                >  1:1646204/1‑98 (MQ=255)                                                 ggggAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGc                                              >  1:225415/1‑100 (MQ=255)                                                        tGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGATTTTGAAAGCATCCGTTGCTACGACTCGCACAAAgg                                       >  2:684751/1‑100 (MQ=255)                                                           ttCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGAcc                                    <  1:24663/100‑1 (MQ=255)                                                             cGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCgg                                  >  1:960947/1‑100 (MQ=255)                                                              gCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGTACCGGt                                 >  1:1067326/1‑100 (MQ=255)                                                                tGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTg                               <  2:923894/100‑1 (MQ=255)                                                                tGGGAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTg                               <  2:39267/100‑1 (MQ=255)                                                                 gggAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGt                              <  1:1454069/100‑1 (MQ=255)                                                                  ggAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTACACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTa                             >  1:1387423/1‑100 (MQ=255)                                                                   gAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTAt                            >  2:1696716/1‑100 (MQ=255)                                                                   gAAGACGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTAt                            <  1:1767682/100‑1 (MQ=255)                                                                     aGACGCGAAGGGGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGTTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTAttn                          <  1:848043/100‑2 (MQ=255)                                                                       aCGCGAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCg                        <  1:380038/100‑1 (MQ=255)                                                                        cgcgAAGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTcc                         >  2:1243473/1‑98 (MQ=255)                                                                             aGGTGCATGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCg                  <  2:1101130/100‑1 (MQ=255)                                                                                   aTGTGATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCa            <  2:619859/100‑1 (MQ=255)                                                                                       gATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATg        >  1:202868/1‑100 (MQ=255)                                                                                       gATGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCAATCGTGAGAATATg        >  2:230918/1‑100 (MQ=255)                                                                                        aTGTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGc       <  2:1098311/100‑1 (MQ=255)                                                                                          gTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAg     >  2:992117/1‑100 (MQ=255)                                                                                          gTCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAg     <  2:487314/100‑1 (MQ=255)                                                                                           tCGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGc    <  1:551513/100‑1 (MQ=255)                                                                                            cGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCg   <  2:1066266/100‑1 (MQ=255)                                                                                            cGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCg   >  2:796672/1‑100 (MQ=255)                                                                                            cGCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCg   >  1:1066256/1‑100 (MQ=255)                                                                                             gCACGTGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCGt  >  1:976689/1‑100 (MQ=255)                                                                                                  |                                                                                               AGGAATATAAAAATGACCACGAAGAAAGCTGATTACATTTGGTTCAATGGGGAGATGGTTCGCTGGGAAGACGCGAAGGTGCATGTGATGTCGCACGCGCTGCACTATGGCACTTCGGTTTTTGAAGGCATCCGTTGCTACGACTCGCACAAAGGACCGGTTGTATTCCGCCATCGTGAGCATATGCAGCGT  >  NC_000913/3952472‑3952663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑