Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_004302	13,763	T→C	V122A (GTT→GCT)	r1tp24 →	ORF24

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_004302	13,763	0	T	C	98.7%	200.1 / ‑4.1	76	V122A (GTT→GCT)	r1tp24	ORF24
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (73/2);  minor base G (1/0);  total (74/2)
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

AAGATGAAGTGAATACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGTTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACTTAGCAG  >  NC_004302/13694‑13835                                                                         |                                                                          caGATGAAG‑GAATACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCAtt                                                                     >  1:13681095/2‑75 (MQ=255)  cctgaatgTGAATACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCAtt                                                                     >  1:2934794/8‑75 (MQ=255)     gttagaaaaTAAAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTaaa                                                                  >  1:7658676/8‑75 (MQ=255)     gttaGTGAATA‑AAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTaaaa                                                                 >  1:5141931/4‑75 (MQ=255)       agagcaaTACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAG‑T‑CAAGC‑AAAGA‑GTTAGCTGCATTAAAACtt                                                              >  1:9163549/6‑75 (MQ=255)       agagcaaTACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAG‑T‑CAAGC‑AAAGA‑GTTAGCTGCATTAAAACtt                                                              >  1:6268159/6‑75 (MQ=255)           taaggaaaaTCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGa                                                            >  1:8580117/7‑75 (MQ=255)            tagaaaaaTCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGaa                                                           >  1:10348204/6‑75 (MQ=255)               cttgggtcTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGaacaa                                                        >  1:1838663/8‑75 (MQ=255)               cgagaTCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGaacaa                                                        >  1:4497955/5‑75 (MQ=255)               atgggtgcTAAT‑AGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATAAAAACTTGaacaac                                                       >  1:12144971/8‑75 (MQ=255)                 ttgtagtaataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:11188654/7‑75 (MQ=255)                 gcagaataataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:13565048/7‑75 (MQ=255)                 gagatgtaataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACGTGAacaaca                                                      >  1:10956034/7‑75 (MQ=255)                 ccaagcTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:14316476/6‑75 (MQ=255)                 ccaagcTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:14297135/6‑75 (MQ=255)                 actatttaataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:11941024/7‑75 (MQ=255)                 aatttagaataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAacaaca                                                      >  1:6840161/8‑75 (MQ=255)                  aatacaaataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACAt                                                     >  1:1959603/7‑75 (MQ=255)                   gaggaggtaaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATc                                                    >  1:10575697/8‑75 (MQ=255)                       tggaaaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTAtt                                                >  1:1932560/5‑75 (MQ=255)                       gggaaaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACCTGAACAACATCtgat                                                >  1:345533/5‑72 (MQ=255)                       atagaaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTact                                                >  1:14468930/5‑73 (MQ=255)                        ggaaaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTa                                               >  1:9665348/4‑75 (MQ=255)                        aataaGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTa                                               >  1:16985932/1‑75 (MQ=255)                              aCTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTatcgtgg                                         <  1:10763057/75‑7 (MQ=255)                               caggcACTATGTATCA‑AGAAGCTCCAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaat                                       >  1:3149981/5‑75 (MQ=255)                               atgttaCTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaat                                       >  1:390761/6‑75 (MQ=255)                                 taaggaaTGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatat                                     >  1:662547/7‑75 (MQ=255)                                 ctcACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatat                                     >  1:6722693/1‑75 (MQ=255)                                  gaagctggTATTA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatata                                    >  1:12338722/8‑75 (MQ=255)                                  cttattcgTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatata                                    >  1:15338994/8‑75 (MQ=255)                                  cgtatgtGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatata                                    >  1:1014077/7‑75 (MQ=255)                                   ttttATGTA‑CA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataat                                  >  1:14648315/4‑75 (MQ=255)                                   tgaaggctATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGTC‑Aaatataa                                   >  1:1988891/8‑75 (MQ=255)                                   gaCTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataa                                   >  1:6537381/2‑75 (MQ=255)                                   acatATGTAT‑A‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataat                                  >  1:12847664/4‑75 (MQ=255)                                    ccgaTGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataat                                  >  1:8985592/4‑75 (MQ=255)                                    attaatcaTCA‑AGAGGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataat                                  >  1:15290726/8‑75 (MQ=255)                                     cTATGTATAATAGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑Aaatataat                                  >  1:1311875/1‑75 (MQ=255)                                       gaagtgta‑agaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATc                               >  1:13577898/8‑75 (MQ=255)                                       attggaaa‑agaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATc                               >  1:2564078/8‑75 (MQ=255)                                        tggggaa‑agatgCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCg                              >  1:90861/7‑75 (MQ=255)                                        tggaaga‑agaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCg                              >  1:4250145/7‑75 (MQ=255)                                         tgcata‑agaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGa                             >  1:8592931/6‑75 (MQ=255)                                         ggtacA‑AGAAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGa                             >  1:1814444/5‑75 (MQ=255)                                           tgtaatgaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGAt                            >  1:10292497/7‑75 (MQ=255)                                           atttagtaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGAt                            >  1:3208778/8‑75 (MQ=255)                                           agggcttaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGAt                            >  1:10625722/8‑75 (MQ=255)                                           aacA‑AGCAGCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATg                           >  1:14874848/3‑75 (MQ=255)                                            tgtgagaaaCTACAAGC‑AAAGA‑GTTAGGTGCATTAATACTAGAACAACATCTATTAGAC‑AAATATATAATCGATg                           >  1:12306343/5‑75 (MQ=255)                                            tgtgagaaaCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATg                           >  1:15191968/5‑75 (MQ=255)                                             tcattaggCTAC‑AGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGtt                         >  1:12813273/8‑75 (MQ=255)                                               atgaagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGttt                        >  1:16867327/3‑75 (MQ=255)                                                gggcacTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTta                       >  1:7351382/6‑75 (MQ=255)                                                 tcagCTACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTtat                      >  1:8145513/3‑75 (MQ=255)                                                 caggttACAGGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTtat                      >  1:12651473/6‑75 (MQ=255)                                                  tgttagcAAGCAAAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTtat                      >  1:10477764/7‑75 (MQ=255)                                                  tatcTACATGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTtata                     >  1:1556159/4‑75 (MQ=255)                                                  gccatataaGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTtata                     >  1:14815289/8‑75 (MQ=255)                                                  ataagtgaaGC‑AAAGA‑GTTAGCTGCATTGAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGACGTTtata                     >  1:2622211/8‑75 (MQ=255)                                                   ttttACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATaa                    >  1:5439652/4‑75 (MQ=255)                                                   atcttaaaGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATaa                    >  1:6974623/7‑75 (MQ=255)                                                      tACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACa                 >  1:12308331/1‑75 (MQ=255)                                                      tACAAGC‑AAAGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATATTtaaacccc                 <  1:8075625/75‑7 (MQ=255)                                                       tgtgac‑AAATA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaa                >  1:11429846/6‑75 (MQ=255)                                                       ccAAGC‑ATACA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaa                >  1:13403719/2‑75 (MQ=255)                                                       aattac‑AAAGA‑GTTAGCTGCATTAAAAC‑TGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaaa               >  1:15348572/6‑75 (MQ=255)                                                       aatgatgaaaGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACa                 >  1:6761951/8‑75 (MQ=255)                                                        acttagaaaGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaa                >  1:7596375/7‑75 (MQ=255)                                                          gataaaaGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaaaa              >  1:36221/5‑75 (MQ=255)                                                          atcaaaaGA‑GTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACaaaa              >  1:15312503/5‑75 (MQ=255)                                                            ggtaata‑gttagctGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATc            >  1:1921648/7‑75 (MQ=255)                                                            ggaaaGA‑GTGAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATc            >  1:3850302/3‑75 (MQ=255)                                                             taaaGAGGTTAGCTGCATTAAAACTTGAACAACATCTATTAGACAAAATATAATATCGATGTTTATAAACAAAAt             >  1:13600441/2‑75 (MQ=255)                                                               tgga‑gTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCAc         >  1:1325703/3‑75 (MQ=255)                                                               gtga‑gTTAGCTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCAc         >  1:11645087/3‑75 (MQ=255)                                                                ttcaggaagttGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCAc         >  1:15283710/8‑75 (MQ=255)                                                                gagctaaagttGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCAc         >  1:15794843/8‑75 (MQ=255)                                                                cta‑gttagctGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACt        >  1:15467154/3‑75 (MQ=255)                                                                cta‑gttagctGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACt        >  1:9757067/3‑75 (MQ=255)                                                                 aaggttagctGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACt        >  1:17004396/4‑75 (MQ=255)                                                                 aaggttagctGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACt        >  1:17196754/4‑75 (MQ=255)                                                                  cggttctttGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACtt       >  1:4227044/8‑75 (MQ=255)                                                                   agatagttGAATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACTTa      >  1:16053634/4‑75 (MQ=255)                                                                      aatttGCA‑TAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACTTAGCag  >  1:3752809/4‑75 (MQ=255)                                                                         |                                                                          AAGATGAAGTGAATACAAATCCTAATAAGACTCTCACTATGTATCA‑AGAAGCTACAAGC‑AAAGA‑GTTAGTTGCATTAAAACTTGAACAACATCTATTAGAC‑AAATATAATATCGATGTTTATAAACAAAATCCACTTAGCAG  >  NC_004302/13694‑13835

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑