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	100.0%	160.6 / NA	64	L110V (CTT→GTT)	r1tp09	ORF9
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (63/1);  total (63/1)

CGTTAAAAAAATTACTCAACTC‑AATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACGACTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTT  >  NC_004302/5170‑5298                                                                      |                                                              ggtaaaaaaaaTTACTCAACTCAAATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACaagttgact                                                         >  1:11125682/5‑75 (MQ=255)          gtaaatacaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTaaa                                               >  1:4305742/8‑75 (MQ=255)           gcggagaaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAAt                                              >  1:12353659/8‑75 (MQ=255)            agggaatactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATg                                             >  1:9506892/8‑75 (MQ=255)            acttttaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATg                                             >  1:12506636/7‑75 (MQ=255)              ggcctggtc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGaa                                           >  1:3188328/8‑75 (MQ=255)               tcaaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAg                                          >  1:16516111/4‑75 (MQ=255)               agtcactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAg                                          >  1:11542206/5‑75 (MQ=255)                gctactc‑atTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:727811/4‑75 (MQ=255)                cagactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:6150945/4‑75 (MQ=255)                 tagtaagaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:14358604/8‑75 (MQ=255)                 gtgtaaaaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:3042486/8‑75 (MQ=255)                 cctggggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:1513639/8‑75 (MQ=255)                 cctggggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc                                         >  1:11440373/8‑75 (MQ=255)                  tagggggaTAGTGATTATGACGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGACGCt                                        >  1:913612/8‑75 (MQ=255)                  tagggggaTAGTGATTATGACGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGACGCt                                        >  1:12117749/8‑75 (MQ=255)                   tgctaaataatGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa                                       >  1:9320870/6‑75 (MQ=255)                   gcttccttAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa                                       >  1:4685281/8‑75 (MQ=255)                   gcttccttAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa                                       >  1:10019461/8‑75 (MQ=255)                   cctaataTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa                                       >  1:1911903/7‑75 (MQ=255)                   actttaaTAGGGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa                                       >  1:11148269/6‑75 (MQ=255)                    catattgaGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa                                      >  1:12127715/8‑75 (MQ=255)                    catattgaGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa                                      >  1:17139487/8‑75 (MQ=255)                    atc‑aaTAGTGATTATGATGAACGCAGACGA‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAAt                                     >  1:16678326/2‑75 (MQ=255)                    aaggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa                                      >  1:16356460/5‑75 (MQ=255)                     actatatgTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAAt                                     >  1:3898888/8‑75 (MQ=255)                       taagtgTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGt                                   >  1:2523448/6‑75 (MQ=255)                       ggtaaGTGA‑TATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTa                                  >  1:5993510/5‑75 (MQ=255)                         gcatagATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAg                                 >  1:3268353/6‑75 (MQ=255)                          ccaatcttATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGt                                >  1:11347226/7‑75 (MQ=255)                          aaaggATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGt                                >  1:1633280/5‑75 (MQ=255)                            ttGATTATAATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGttt                              >  1:4680211/2‑75 (MQ=255)                             gggatATGATGCACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTa                             >  1:2971737/5‑75 (MQ=255)                              ttcaatgaagAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGGAAATGAAGCTAATGTAGTTTAt                            >  1:14397658/5‑75 (MQ=255)                               cgagggttgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATg                           >  1:16256001/8‑75 (MQ=255)                               aTTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATg                           >  1:15648946/1‑75 (MQ=255)                                atatagtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATgg                          >  1:10162370/7‑75 (MQ=255)                                 ttcgaagaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg                         >  1:5193779/7‑75 (MQ=255)                                 tATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg                         >  1:1494027/1‑75 (MQ=255)                                 tATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg                         <  1:1269944/75‑1 (MQ=255)                                  taagtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGc                        >  1:3729874/5‑75 (MQ=255)                                  attatacaCGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGc                        >  1:8599473/8‑75 (MQ=255)                                     gtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCttt                     >  1:15269382/2‑75 (MQ=255)                                     cgtaaCGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCttt                     >  1:12047984/4‑75 (MQ=255)                                       tttatttgACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt                   >  1:2750890/8‑75 (MQ=255)                                       acgcGCAGACGGAAAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTc                    >  1:3947649/4‑75 (MQ=255)                                          agaagaggg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgt                >  1:13575822/8‑75 (MQ=255)                                           gtggtaag‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgta               >  1:4346066/8‑75 (MQ=255)                                           gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag              >  1:12223935/7‑75 (MQ=255)                                           gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag              >  1:10984602/7‑75 (MQ=255)                                           gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag              >  1:11004865/7‑75 (MQ=255)                                           acatgttg‑AAAACAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgta               >  1:11291704/8‑75 (MQ=255)                                            ctcgagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtag              >  1:10934604/6‑75 (MQ=255)                                            cgctagg‑AATGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtag              >  1:12038132/6‑75 (MQ=255)                                              atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta            >  1:12795405/4‑75 (MQ=255)                                              atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta            >  1:7275243/4‑75 (MQ=255)                                              atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta            >  1:11269103/4‑75 (MQ=255)                                               gaagaaaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagat            >  1:15445413/6‑73 (MQ=255)                                                aactcaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAACTAATGTAGTTTATGGGCTTTCTGGtagtag           >  1:15870132/6‑75 (MQ=255)                                                 tgagaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGa          >  1:15262937/5‑75 (MQ=255)                                                 ccttactcAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGa          >  1:4997243/8‑75 (MQ=255)                                                  ggtgaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAt         >  1:1269347/5‑75 (MQ=255)                                                   gcaaGCAGAATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAtt        >  1:4878662/3‑75 (MQ=255)                                                       gagggATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCt    >  1:16281584/4‑75 (MQ=255)                                                         tgaggctGAACGAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCttt  >  1:4538497/7‑75 (MQ=255)                                                                      |                                                              CGTTAAAAAAATTACTCAACTC‑AATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACGACTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTT  >  NC_004302/5170‑5298

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑