Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_004302	9,972	C→A	A59E (GCA→GAA)	r1tp18 →	ORF18

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_004302	9,972	0	C	A	98.6%	168.5 / ‑3.3	69	A59E (GCA→GAA)	r1tp18	ORF18
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (67/1);  minor base T (0/1);  total (67/2)
Fisher's exact test for biased strand distribution p-value = 2.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ATTATGGATAAAGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑CAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCAAACTTCCAGCTTCT  >  NC_004302/9901‑10030                                                                            |                                                              aTTATGGATAAAGAATGGG‑AAAGA‑CCCT‑‑AAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑Aaaaa                                                           >  1:5004994/1‑75 (MQ=255)  tgtgagATAGAGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑Aaaaa                                                           >  1:12890175/6‑75 (MQ=255)   ttaattaaaaGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑aaaaaa                                                          >  1:14258289/8‑75 (MQ=255)     atgATAAAGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAAca                                                        >  1:3831580/3‑74 (MQ=255)       taagaataaTGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aa                                                     >  1:4869782/8‑75 (MQ=255)       gaagaataaTGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aa                                                     >  1:4869774/8‑75 (MQ=255)       agtAAAGAATGGG‑AAAGA‑CCCTAAAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑a                                                      >  1:4706992/3‑75 (MQ=255)       aaattggAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aa                                                     >  1:12233157/7‑75 (MQ=255)        ctgaatgaTGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aaa                                                    >  1:4393601/8‑75 (MQ=255)        attttgAATGCG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aaa                                                    >  1:13805637/6‑75 (MQ=255)        aacgaaaaTGGGAAAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aa                                                     >  1:11972616/7‑75 (MQ=255)        aacgaaaaTGGGAAAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑aa                                                     >  1:2756283/7‑75 (MQ=255)         tcagcgttGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAag                                                   >  1:3769346/8‑75 (MQ=255)         tAAAGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑Taaaaaaagatt                                                    <  1:11786370/75‑7 (MQ=255)         atttaactGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAag                                                   >  1:11824166/8‑75 (MQ=255)         ataaGAGTGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAag                                                   >  1:12181641/3‑75 (MQ=255)         agatagaTGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAag                                                   >  1:302661/7‑75 (MQ=255)            tgaggttg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGc                                                >  1:13178713/8‑75 (MQ=255)            ggtgtaag‑AAAGA‑CCCTAAAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAGAAAAAAACT‑AAaga                                                  >  1:16800750/8‑75 (MQ=255)            gagtaagg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGc                                                >  1:13816673/7‑75 (MQ=255)             acgaggg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAagagat                                               >  1:7983613/5‑73 (MQ=255)               tcagg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCCATTTTAAAT‑AAG‑AAAAAACT‑AAAGAGCTT‑At                                           >  1:14776887/4‑75 (MQ=255)               gaagg‑AAAAA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑a                                            >  1:6228633/4‑75 (MQ=255)               aTGGG‑ATAGACCCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCtt                                              >  1:15431081/1‑75 (MQ=255)                gtagaaaaGA‑CCCT‑AAAAAAGCTAACCCTAATTATAGGCACGCTATTTTAAATAAAG‑AAAAAACT‑AATGAGCTT‑a                                            >  1:16143998/6‑75 (MQ=255)                 tgg‑AAAGA‑CCCT‑AAAAAAGCCAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATg                                          >  1:4778206/2‑75 (MQ=255)                 ccgaagaGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ac                                           >  1:12459101/7‑74 (MQ=255)                 atg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATg                                          >  1:1632021/3‑75 (MQ=255)                 atg‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATg                                          >  1:4438321/3‑75 (MQ=255)                 acaggcaGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑At                                           >  1:11653731/7‑75 (MQ=255)                      cttccgccT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGaa                                       >  1:16234448/7‑75 (MQ=255)                       ggatcccT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAAc                                      >  1:8196397/5‑75 (MQ=255)                        ttgcttt‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACa                                     >  1:10193344/7‑75 (MQ=255)                          gttaaaaaaaaaGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaa                                    >  1:16892395/7‑75 (MQ=255)                          gttaaaaaaaaaGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaa                                    >  1:13111803/7‑75 (MQ=255)                           ggcT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTTGGTGGAACaag                                   >  1:7361109/3‑74 (MQ=255)                           cccT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAGAAAAAAACT‑AAAGAGCTT‑ATGGAACaaa                                   >  1:16596921/1‑75 (MQ=255)                            agtaaaaaaaGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaa                                  >  1:2463715/5‑75 (MQ=255)                            aaaaccaaaaACTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaa                                  >  1:2913728/7‑75 (MQ=255)                            aaaaccaaaaACTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaa                                  >  1:8278127/7‑75 (MQ=255)                             ttttcagaaGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAGAAAAAAACT‑AAAGAGCTT‑ATGGAACaaaa                                  >  1:6388884/8‑75 (MQ=255)                             gt‑AAAAATGTTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaagat                                >  1:9784700/2‑72 (MQ=255)                             ggggcaaaaGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaag                                 >  1:8718242/6‑75 (MQ=255)                             cgaataaaaGTTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaag                                 >  1:16522235/6‑75 (MQ=255)                                 tattaaatAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACtaaaa‑aaaa                            >  1:3220937/8‑75 (MQ=255)                                  tgttagtAACGCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaaa‑aaaaa                           >  1:9837094/7‑75 (MQ=255)                                  gtagaagaaCCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACgaaaa‑aaaaa                           >  1:15292973/8‑75 (MQ=255)                                  ggctgCTAA‑CCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaag‑aaaaaa                          >  1:5429522/5‑75 (MQ=255)                                   tgagtagaCCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaag‑aaaaaa                          >  1:13081364/8‑75 (MQ=255)                                    agacTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACaaaag‑aaaaaag                         >  1:848410/4‑75 (MQ=255)                                     tccTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACgaaaa‑aaaaaaga                        >  1:16594480/3‑75 (MQ=255)                                       actggattAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAaagaag                      >  1:8604786/8‑75 (MQ=255)                                         ggaccTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACgaaaa‑aaaaaagatcgg                    >  1:3697920/4‑71 (MQ=255)                                         aaCCCTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAAcaaaa‑‑aaaaaagatcgga                   >  1:4608099/1‑70 (MQ=255)                                          aCCCTAATTAAAAGAAGGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAActaaa‑‑aaaaaagaaatcgc                  <  1:5952848/75‑6 (MQ=255)                                           ggtgttatatAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAgcg                  >  1:16065500/7‑75 (MQ=255)                                           gccTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAT‑AAAAAAGAagagag                  >  1:12521872/2‑73 (MQ=255)                                           gccTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAgcg                  >  1:10906907/2‑75 (MQ=255)                                           gccTAAATATAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAACAgcg                  >  1:3641899/2‑75 (MQ=255)                                           gaggcaaTAAAAGCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAgcg                  >  1:8813662/6‑75 (MQ=255)                                            aatttatatAA‑CACGCTATTTTAAATAAAGAAAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAgcgc                 >  1:8196978/6‑75 (MQ=255)                                             gtacatctaAGGACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCa                >  1:6402674/8‑75 (MQ=255)                                             cgcatagtaAGGACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCa                >  1:5263403/8‑75 (MQ=255)                                              agatcttaAGCACGCTATTTTAAATAAAGAAAAAAACT‑AAAGAGCTT‑ATGGAACAAAAGAAAAAAAGAAGAgcgc                 >  1:12018175/7‑75 (MQ=255)                                               agaactaAGGACGCTATTTTAAATAAAGAAAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCaa               >  1:9349997/6‑75 (MQ=255)                                                   tcccgCACGCTATTTTAAATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAATGAAGAGCGCAAACTTc          >  1:11977173/5‑75 (MQ=255)                                                   taagagaCGCTATTTTAAATAAAG‑AAAAAACTAAAAGAGCTT‑ATGGAACAAAAGAAAAAAAGAAGAGCGCAAACt            >  1:6405095/7‑75 (MQ=255)                                                       gacagCTATTTTAAATATAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCAAACTTCCAGc      >  1:3918081/5‑75 (MQ=255)                                                         tagtatttttAGATAAAG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCAAACTTCCAGCtt    >  1:7223243/7‑75 (MQ=255)                                                           aaattgataaataaaG‑AAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCAAACTTCCAGCTTCt  >  1:9089356/8‑75 (MQ=255)                                                                            |                                                              ATTATGGATAAAGAATGGG‑AAAGA‑CCCT‑AAAAAAGCTAACCCTAAATATAAGCACGCTATTTTAAATAAAG‑CAAAAACT‑AAAGAGCTT‑ATGGAACAAAAG‑AAAAAAGAAGAGCGCAAACTTCCAGCTTCT  >  NC_004302/9901‑10030

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑