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	88.0%	71.3 / 3.8	25	noncoding (71/87 nt)	leuT	tRNA‑Leu
Reads supporting (aligned to +/- strand):  ref base . (2/1);  new base C (11/11);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGATTGTGATTCCAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑C‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCCTCTCTCGCCGAC  >  NC_000913/3982538‑3982809                                                                                                                                            |                                                                                                                                       ggATTGTGATTCCAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑c                                                                                                                                       >  1:641960/1‑140 (MQ=255)       tgATTCCAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑c‑cccccc                                                                                                                                >  1:90719/1‑140 (MQ=255)            ccAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑c‑cccccccctcg                                                                                                                           <  2:90719/140‑5 (MQ=255)            ccAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTAAGGTGTTAGTGTGCTTCCGGACGTGAGGGTACAAGT‑c‑cccccccctcg                                                                                                                           >  2:229380/1‑136 (MQ=25)                 tGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGcacca                                                                                                                       >  2:9157/1‑140 (MQ=255)                      tGGGTTCGAATCCCAATAGCCACCCAATTGTTAGAAGGTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACt                                                                                                                  <  1:356321/140‑1 (MQ=18)                                 cccATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTg                                                                                                       <  1:9157/140‑1 (MQ=255)                                     ttAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAGGT‑CGCCCTCCCTCGCAGCACGACTTTAAAGAATTGAACt                                                                                                   >  2:189380/1‑140 (MQ=21)                                            ccccATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACAACTTTAAAGAATTGAACTAAAAAtt                                                                                            >  1:279683/1‑140 (MQ=255)                                                attattAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCaaa                                                                                        <  2:596948/140‑1 (MQ=255)                                                  tattaGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTGGCAACACGACTTTAAAAAATTTAACTAAAAATTCaaaaa                                                                                      >  2:306108/1‑140 (MQ=18)                                                        aaGTTGTGACAATGCGAAGGTGGCGTAATGGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTa                                                                                <  1:306108/140‑1 (MQ=255)                                                          gTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑C‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTAttt                                                                             >  1:465074/1‑140 (MQ=255)                                                             gtgACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCg                                                                           >  2:155519/1‑140 (MQ=255)                                                             gtgACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCg                                                                           >  1:526097/1‑140 (MQ=255)                                                                    tGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑C‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAg                                                                   <  2:465074/140‑1 (MQ=255)                                                                       gAAGGTGGCGGAATTGGTAGACTCGCTAGCTTCGGTTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAgcg                                                                 <  2:317636/140‑1 (MQ=25)                                                                       gAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAgcg                                                                 <  1:472284/140‑1 (MQ=255)                                                                                       gTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCaa                                                 <  2:711297/140‑1 (MQ=255)                                                                                        tAGACGCGCTAGCTTCAGGTGTCAGCGTCCTTACGGAAGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAAc                                                <  1:189380/140‑1 (MQ=37)                                                                                            cgcgCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGt                                            >  1:435705/1‑140 (MQ=255)                                                                                            cgcgCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGAGAGAAGCGCAGCTCGGTAGCGCAACTGGt                                            >  1:333863/1‑140 (MQ=37)                                                                                                cTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTgg                                        <  2:526097/140‑1 (MQ=255)                                                                                                                              gTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCGGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCctctc          >  2:721548/1‑140 (MQ=255)                                                                                                                              gTGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCctctc          >  2:25368/1‑140 (MQ=255)                                                                                                                               tGGGGGTTCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGATAGCGCAACTGGCTTGCAACCAGTGAGTCGGGGGTTCGAGTCctctcc         >  2:347606/1‑139 (MQ=255)                                                                                                                               tGGGGGTTCAAGTCC‑CCCCCCCCCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGCCGGAGGTTCGAATCctctct         >  1:62817/1‑140 (MQ=255)                                                                                                                                      tCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCCTCTCTCGCCGAc  <  1:155519/140‑1 (MQ=255)                                                                                                                                      tCAAGTCC‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCCTCTCTCGCCGAc  <  2:435705/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                       GGATTGTGATTCCAGTTGTCGTGGGTTCGAATCCCATTAGCCACCCCATTATTAGAAGTTGTGACAATGCGAAGGTGGCGGAATTGGTAGACGCGCTAGCTTCAGGTGTTAGTGTCCTTACGGACGTGGGGGTTCAAGT‑C‑CCCCCCCTCGCACCACGACTTTAAAGAATTGAACTAAAAATTCAAAAAGCAGTATTTCGGCGAGTAGCGCAGCTTGGTAGCGCAACTGGTTTGGGACCAGTGGGTCGGAGGTTCGAATCCTCTCTCGCCGAC  >  NC_000913/3982538‑3982809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑