BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_004302	5,237	C→G	L110V (CTT→GTT)	r1tp09 →	ORF9

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_004302	5,237	0	C	G	92.9%	64.4 / ‑1.1	29	L110V (CTT→GTT)	r1tp09	ORF9
Reads supporting (aligned to +/- strand): ref base C (1/0); major base G (25/1); minor base T (2/0); total (28/1)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

TTAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑CGACTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTAACA  >  NC_004302/5172‑5302

gtAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAg                                                          >  1:4098499/2‑75 (MQ=255)

gtAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAg                                                          >  1:17006994/2‑75 (MQ=255)

      tgttgagtcaactcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTaa                                                    >  1:9869790/8‑75 (MQ=255)

         taaatatactcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATg                                                 >  1:16779127/8‑75 (MQ=255)

           cgagatctcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGAAGTAAATGaa                                               >  1:8076379/7‑75 (MQ=255)

                tggttttAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTaa                                          >  1:6610009/7‑75 (MQ=255)

                ggatcgtAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAAGCAGTTT‑GACTTAGCAGTAAATGAAGCTa                                           >  1:16454581/7‑75 (MQ=255)

                ggatcgtAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAAGCAGTTT‑GACTTAGCAGTAAATGAAGCTa                                           >  1:6873848/7‑75 (MQ=255)

                  ggaagaGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATg                                        >  1:14583510/6‑75 (MQ=255)

                   tgctgatGATTCTGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGt                                       >  1:315741/7‑75 (MQ=255)

                   caaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGcaagatc                                       >  1:1753292/1‑69 (MQ=255)

                     aggtgagttATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAg                                     >  1:12447066/8‑75 (MQ=255)

                      cggccgatATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGt                                    >  1:13330801/8‑75 (MQ=255)

                      aatccgttATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGt                                    >  1:3128087/7‑75 (MQ=255)

                       gcagATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtt                                   >  1:8869797/4‑75 (MQ=255)

                       gagaatcatgatgAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtt                                   >  1:16310036/8‑75 (MQ=255)

                           agggttttgaATGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATg                               >  1:2962984/8‑75 (MQ=255)

                            ctgctatgaACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATgg                              >  1:6747262/6‑75 (MQ=255)

                             tATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtcttttat                             <  1:2453427/75‑8 (MQ=255)

                             actagtgaACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg                             >  1:481304/6‑75 (MQ=255)

                                tttttttgCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCtt                          >  1:5006996/8‑75 (MQ=255)

                                   cgtagCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt                       >  1:16559602/5‑75 (MQ=255)

                                   ataCGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt                       >  1:2118373/3‑75 (MQ=255)

                                   agaatcAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt                       >  1:1079053/6‑75 (MQ=255)

                                         gacacgAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagt                 >  1:15783342/6‑75 (MQ=255)

                                          gcatgtgaGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta                >  1:5406262/8‑75 (MQ=255)

                                             caggataaGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAt             >  1:12250339/8‑75 (MQ=255)

                                                aaGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTg          >  1:63029/1‑75 (MQ=255)

                                                          gtcttcGACTTAGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTaaca  >  1:5123467/6‑75 (MQ=255)

TTAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑CGACTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTAACA  >  NC_004302/5172‑5302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`