Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,982,684	(C)8→9	noncoding (79/87 nt)	leuT →	tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,982,676	1	.	C	83.7%	125.4 / 21.2	44	noncoding (71/87 nt)	leuT	tRNA‑Leu
Reads supporting (aligned to +/- strand):  ref base . (3/4);  new base C (21/15);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 6.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGG  >  NC_000913/3982579‑3982772                                                                                                   |                                                                                                  cACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cc                                                                                                 >  2:806215/1‑100 (MQ=255)   ccccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑ccc                                                                                                <  2:226140/99‑1 (MQ=255)    cccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cccc‑c                                                                                             >  1:665733/1‑100 (MQ=255)    cccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cccc‑c                                                                                             >  1:639655/1‑100 (MQ=255)    cccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCATTACGGACGTGGGGGTTCAAGT‑gcc                                                                                                >  2:120633/1‑98 (MQ=255)     ccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cccc‑cc                                                                                            >  2:197861/1‑100 (MQ=255)     ccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAACT‑cccc‑cc                                                                                            <  1:687758/100‑1 (MQ=255)       attattAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cccc‑cccc                                                                                          >  2:1060278/1‑100 (MQ=255)           ttaGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑cccc‑ccccctcg                                                                                      >  2:949299/1‑96 (MQ=255)             aGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGca                                                                                     <  2:738780/100‑1 (MQ=255)                aGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGcacca                                                                                  >  1:1275482/1‑100 (MQ=255)                  ttGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACg                                                                                >  1:280359/1‑100 (MQ=255)                    gtgACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGAc                                                                              >  1:207907/1‑100 (MQ=255)                     tgACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACt                                                                             <  1:741107/100‑1 (MQ=255)                      gACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACttt                                                                           >  1:137925/1‑100 (MQ=255)                         aaTGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGATAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTaa                                                                         <  2:832505/100‑1 (MQ=255)                          aTGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTaaa                                                                        >  2:131006/1‑100 (MQ=255)                                   tGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAAc                                                               <  2:1180728/100‑1 (MQ=255)                                            tGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCa                                                     <  1:476452/100‑1 (MQ=255)                                             ggTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCa                                                     >  2:380866/1‑100 (MQ=255)                                               tAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaa                                                   >  2:1298777/1‑100 (MQ=255)                                               tAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaa                                                   >  2:1185198/1‑100 (MQ=255)                                               tAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaaa                                                  >  2:705567/1‑100 (MQ=255)                                                aGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGCGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaaa                                                  <  2:917924/100‑1 (MQ=255)                                                 gACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaaaa                                                 >  2:1214447/1‑100 (MQ=255)                                                     cgcTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAg                                             <  2:207905/100‑1 (MQ=255)                                                      gcTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGTGGGTTCAATT‑CCCCACTCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTTAAAAAGc                                               <  2:183879/97‑1 (MQ=21)                                                      gcTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGt                                            >  2:1252490/1‑100 (MQ=255)                                                       cTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTa                                           >  1:733053/1‑100 (MQ=255)                                                           cTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTc                                       <  2:639651/100‑1 (MQ=255)                                                            ttCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCg                                      <  2:308069/100‑1 (MQ=255)                                                            ttCAGGTGTTAGTGTCCTTACGGACGTGGGGGGTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCg                                      >  1:808362/1‑100 (MQ=255)                                                               aGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGa                                  >  2:551008/1‑100 (MQ=255)                                                                ggTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGa                                  <  1:1298788/100‑1 (MQ=255)                                                                ggTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGa                                  >  2:117887/1‑100 (MQ=255)                                                                   gtTAGTGTCCTTACGGACGTGGGGGTTCAAGTGCCAC‑CCGCTCGCACCACTGCGTTCAAGAATTGCACTAAAACTTCAAAAAGCAGTATTTAGGctcgt                                >  2:1302671/1‑95 (MQ=16)                                                                      aGTGTCCTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAgcg                            >  1:559914/1‑100 (MQ=255)                                                                            cTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCtt                      >  2:283590/1‑100 (MQ=255)                                                                            cTTACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCtt                      >  2:653344/1‑100 (MQ=255)                                                                              tACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTgg                    >  2:134995/1‑100 (MQ=255)                                                                              tACGGACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTgg                    <  1:1060288/100‑1 (MQ=255)                                                                                 ggACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAg                 <  1:380869/100‑1 (MQ=255)                                                                                 ggACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAg                 <  1:1252501/100‑1 (MQ=255)                                                                                  gACGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAgc                >  2:127338/1‑100 (MQ=255)                                                                                    cGTGGGGGTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAgcgc              <  2:192630/100‑1 (MQ=255)                                                                                     gTGGGGGTCCAAGC‑CCCCACCCATCGCACCACGACTTTAAAGAATTGAAAAAAAAAAAAAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAgcgc              <  2:192582/99‑1 (MQ=255)                                                                                       gggggTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAAc           >  2:744030/1‑100 (MQ=255)                                                                                        ggggTTCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACt          <  1:382087/100‑1 (MQ=255)                                                                                            ttCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTGTTTCGCCGAGTAGCCCAGCTTGGTAGCGCAACTGGtt      >  2:879444/1‑100 (MQ=255)                                                                                            ttCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGtt      <  2:280356/100‑1 (MQ=255)                                                                                             tCAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGttt     >  1:288980/1‑100 (MQ=255)                                                                                              cAAGTCCCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTg    >  2:645016/1‑100 (MQ=255)                                                                                               aaGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTggg  <  2:137923/100‑1 (MQ=255)                                                                                                   |                                                                                                  CACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑CCCC‑CCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGG  >  NC_000913/3982579‑3982772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑