Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,712,402	A→G	S121S (AGT→AGC)	trmN ←	tRNA1(Val) (adenine(37)‑N6)‑methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,712,402	0	A	G	97.1%	239.2 / ‑1.9	69	S121S (AGT→AGC)	trmN	tRNA1(Val) (adenine(37)‑N6)‑methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (38/29);  total (39/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

AGGTCAGCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTACTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGTT  >  NC_000913/2712305‑2712497                                                                                                  |                                                                                                aGGTCAGCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCt                                                                                               <  2:1154849/100‑1 (MQ=255)    tCAGCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCtgat                                                                                            <  2:1348110/100‑1 (MQ=255)       gCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTgatgat                                                                                         <  2:1542631/100‑1 (MQ=255)       gCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTgatgat                                                                                         >  2:545524/1‑100 (MQ=255)          aCGATGGGTGATCAAGCGTAGTGGTATAGCAAGACTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTaa                                                                                      >  2:1033311/1‑100 (MQ=255)           cGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTaaa                                                                                     >  2:591321/1‑100 (MQ=255)                        aGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAACTCGAAGAGTCCTg                                                                        >  1:1074565/1‑100 (MQ=255)                        aGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTg                                                                        <  2:895594/100‑1 (MQ=255)                           gTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTc                                                                      <  2:770519/99‑1 (MQ=255)                              gTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTctgct                                                                  >  1:483079/1‑100 (MQ=255)                               tGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTctgctg                                                                 <  1:117494/100‑1 (MQ=255)                               tGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTctgctg                                                                 <  2:170875/100‑1 (MQ=255)                               tGGTATAGCGAGCCTGTCCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTctgctg                                                                 <  2:1113589/100‑1 (MQ=255)                                ggTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgt                                                                >  2:537919/1‑100 (MQ=255)                                ggTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgt                                                                >  2:412093/1‑100 (MQ=255)                                ggTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgt                                                                >  2:351068/1‑100 (MQ=255)                                 gTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTACTGATGATTAAATCGAAGCGTACTGTCTGCtgtg                                                               <  1:761552/100‑1 (MQ=255)                                  tataGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgtgt                                                              <  2:1421235/100‑1 (MQ=255)                                  tataGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTAATGTCTGCtgtgt                                                              <  1:1033318/100‑1 (MQ=255)                                   ataGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgtgtg                                                             <  2:1398948/100‑1 (MQ=255)                                   ataGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgtgtg                                                             >  2:1549076/1‑100 (MQ=255)                                   ataGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCtgtgtg                                                             >  1:148721/1‑100 (MQ=255)                                    taGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGa                                                            <  1:24691/100‑1 (MQ=255)                                      gCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATc                                                          >  2:726446/1‑100 (MQ=255)                                       cGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATcc                                                         >  2:1242911/1‑100 (MQ=255)                                        gAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCa                                                        >  2:714946/1‑100 (MQ=255)                                           ccggtgcgcGTTGAGGGGTCGAGCAACCTGCTCCCTGCGGACAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCAct                                                      <  2:161752/91‑1 (MQ=255)                                             tGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCActgct                                                   >  1:128730/1‑100 (MQ=255)                                              gTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCActgctg                                                  >  2:52768/1‑100 (MQ=255)                                              gTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCActgctg                                                  >  2:984064/1‑100 (MQ=255)                                              gTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCActgctg                                                  <  1:1430143/100‑1 (MQ=255)                                              gTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCActgctg                                                  >  1:666947/1‑100 (MQ=255)                                               ttCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGa                                                 >  1:1119596/1‑100 (MQ=255)                                               ttCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGa                                                 >  2:432665/1‑100 (MQ=255)                                                 cccGTTGAGGTGTCGAGCACTCTGCTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAat                                               <  1:545527/100‑1 (MQ=255)                                                 cccGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAat                                               <  1:261925/100‑1 (MQ=255)                                                    gTTGAGGTGTCGAGCACTCTCGTCCGTGCTGATCGTAGGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACGCCTTAatat                                             <  2:1074558/99‑1 (MQ=255)                                                      tGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATccg                                          <  2:1571180/100‑1 (MQ=255)                                                         ggTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGGATATccgccg                                       >  2:1030879/1‑100 (MQ=255)                                                         ggTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATccgccg                                       <  2:128730/100‑1 (MQ=255)                                                          gtgtCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGt                                      <  1:705988/100‑1 (MQ=255)                                                           tgtCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTa                                     >  1:819338/1‑100 (MQ=255)                                                           tgtCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTa                                     <  2:1336133/100‑1 (MQ=255)                                                            gtCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTAt                                    >  2:1059118/1‑100 (MQ=255)                                                              cGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATgg                                  >  2:1209883/1‑100 (MQ=255)                                                                 gCACTCTACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACg                               <  2:184534/100‑1 (MQ=255)                                                                    ctctACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTa                            >  1:770869/1‑100 (MQ=255)                                                                    ctatACTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATAGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGTACGTTa                            >  1:379287/4‑100 (MQ=255)                                                                        aCTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATcc                        <  1:612897/100‑1 (MQ=255)                                                                        aCTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATcc                        >  2:773219/1‑100 (MQ=255)                                                                        aCTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATcc                        <  1:1504732/100‑1 (MQ=255)                                                                        aCTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATcc                        <  1:612921/100‑1 (MQ=255)                                                                         cTCCCTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCg                       >  2:1510210/1‑100 (MQ=255)                                                                           cccTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGct                     >  1:756868/1‑100 (MQ=255)                                                                           cccTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGct                     <  1:1549086/100‑1 (MQ=255)                                                                           cccTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGct                     >  2:359846/1‑100 (MQ=255)                                                                           cccTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGct                     <  1:48650/100‑1 (MQ=255)                                                                           cccTGCTGATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGCCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGc                      >  2:762539/1‑99 (MQ=255)                                                                               gctgATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGc                 <  2:1559494/100‑1 (MQ=255)                                                                                  gATAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCa              >  2:1457343/1‑100 (MQ=255)                                                                                    tAGTAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCa              >  2:909934/1‑98 (MQ=255)                                                                                       tAAGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACgggg         >  1:130698/1‑100 (MQ=255)                                                                                         aGGTGGGTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGAc       >  1:508120/1‑100 (MQ=255)                                                                                         aGGTGGGTTGCTGATGATTAAATCGAAGAGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACggg          >  2:935943/1‑97 (MQ=255)                                                                                         aGGTGGGTTACTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGAc       >  1:229479/1‑100 (MQ=255)                                                                                             gggTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGt   >  1:218597/1‑100 (MQ=255)                                                                                             gggTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGt   >  2:87677/1‑100 (MQ=255)                                                                                              ggTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGtt  >  1:165023/1‑100 (MQ=255)                                                                                              ggTTGCTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGtt  <  2:756864/100‑1 (MQ=255)                                                                                                  |                                                                                                AGGTCAGCAACGATGGGTGATCAAGCGTAGTGGTATAGCGAGCCTGTTCCCGTTGAGGTGTCGAGCACTCTACTCCCTGCTGATAGTAAGGTGGGTTACTGATGATTAAATCGAAGCGTACTGTCTGCTGTGTGATCCACTGCTGAATATCCGCCGTATGGACGTTAATCCGCTCTGCCCACGGGGACTGGTT  >  NC_000913/2712305‑2712497

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑