Version 2.22.2
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 2)

Assembly

2693 (1 contig(s))
4809.4
116495
7516.78 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
81.3919
95.1192
1
1

Alignment

segment 2
3359.0 (NT) + 5685.0 (AA) = 9044.0
80.4054
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT12693100%335962.7%2687 (99.8%)2187 (81.2%)0/6
Mutations:
25T>C 26C>A 28A>G 43T>C 50A>G 56C>A 61A>T 62C>A 64A>T 65G>A 70A>C 82A>G 88A>T 91T>C 92A>G 93G>A 94C>G 98A>C 100C>G 101A>G 102T>A 104A>C 106T>A 109T>C 110G>A 112C>T 113_118delAGTCCT 120A>G 122T>A 123C>T 124A>G 133A>T 136A>C 143T>C 145A>T 148T>A 157A>G 160G>A 161A>G 163A>C 164A>G 166T>A 169A>C 172T>C 181A>G 185G>A 193A>T 194T>G 202G>A 205A>G 208A>G 214T>A 216A>C 217T>G 229G>T 235G>A 239T>C 241A>T 247A>T 248C>T 250T>G 262G>A 265A>G 268T>C 278G>A 280T>A 292A>T 304T>G 307C>A 310T>A 335C>T 337C>G 340A>G 346A>G 352C>T 355A>C 361A>G 367A>G 370A>G 376A>G 379A>G 385A>G 388G>A 392C>A 408A>G 412A>G 413T>C 418T>A 430T>A 436A>T 441G>A 446C>T 448T>G 454T>C 469A>G 475A>G 476C>A 477G>A 478A>G 485C>T 487T>A 490T>A 505T>C 521T>C 529A>G 538A>G 541A>T 542T>C 544A>T 546T>C 547G>T 556G>A 563C>T 566T>C 569C>T 571T>A 583T>A 586A>T 589G>A 598T>C 604G>A 613C>T 619A>T 622T>C 634A>G 637C>A 638G>A 639C>G 640A>T 643A>C 646C>T 655T>A 667A>G 673C>A 679T>C 685A>G 697A>T 700T>G 715A>C 718T>A 727T>C 728C>A 730A>G 733T>C 736A>T 745T>C 751T>A 757G>A 766T>A 769C>T 770C>T 772T>C 775G>T 778T>C 781C>T 784A>G 787C>T 790C>T 802G>A 805G>A 808A>T 829C>A 832T>A 844A>T 847A>T 850G>A 853A>G 859A>G 865T>C 868C>T 878T>C 880A>T 892G>A 896T>C 898A>G 901G>A 904T>A 907T>A 919C>A 925A>T 928C>T 931G>A 940T>C 943G>A 944T>C 946A>G 952A>G 955T>C 967G>A 970A>C 971C>T 973C>G 982T>G 988T>A 991A>T 994T>A 997T>C 1004T>C 1006A>G 1015T>G 1018G>A 1021G>A 1024A>G 1027C>T 1028C>T 1033A>G 1042A>T 1045T>A 1048T>C 1051G>A 1054A>G 1060C>T 1063G>A 1072A>G 1085T>C 1087G>A 1093T>A 1096G>A 1105A>G 1111G>A 1114T>G 1144C>G 1147T>A 1153T>C 1159T>C 1166T>C 1174T>A 1177T>A 1183G>A 1189G>A 1201A>G 1202T>C 1204A>T 1213A>G 1216G>T 1225C>T 1232C>T 1234T>A 1243C>T 1255C>A 1261G>A 1262A>G 1264T>G 1273T>C 1279T>C 1285A>G 1294A>G 1297A>T 1303T>C 1309A>G 1312C>T 1316A>G 1318A>G 1324C>A 1327T>A 1328G>A 1330T>A 1336G>A 1339A>G 1352A>C 1366G>A 1369T>C 1372T>A 1384T>A 1387C>A 1393A>G 1396T>A 1402G>A 1405A>G 1411T>A 1420T>C 1429T>G 1436T>C 1438A>G 1447T>C 1451T>A 1453T>C 1459G>A 1474G>T 1483A>T 1486G>A 1489A>G 1495A>G 1498C>A 1499T>C 1507T>C 1513A>T 1522T>A 1528A>C 1529G>A 1531C>T 1534C>T 1537A>G 1540A>G 1546A>G 1550C>T 1552G>A 1559T>C 1564T>A 1565A>C 1579C>A 1588A>T 1600A>G 1603A>G 1606T>A 1609A>C 1613A>C 1615A>T 1621T>A 1624G>A 1625C>T 1630T>A 1633T>A 1636C>T 1639A>G 1648G>A 1649C>T 1651T>A 1654C>T 1663A>T 1666A>G 1669G>A 1673T>G 1675A>T 1681T>C 1684T>C 1687G>A 1691T>C 1702C>T 1703A>G 1705A>T 1708A>G 1720G>A 1729A>G 1732A>T 1735A>G 1741T>A 1750G>A 1753A>G 1759A>T 1765A>C 1768A>G 1771A>G 1774A>G 1783A>T 1789A>T 1795T>A 1798G>C 1807G>C 1810T>C 1816A>G 1822G>A 1825C>T 1828T>C 1831C>T 1840G>T 1846C>T 1882C>T 1888T>G 1891A>C 1894T>A 1903G>A 1906A>T 1913T>C 1927A>G 1930G>A 1933A>G 1939A>G 1940T>G 1951G>A 1954C>T 1958C>T 1960G>A 1972G>C 1975A>T 1978T>C 1984T>A 1987G>T 1993A>T 2002C>T 2017G>A 2020A>G 2027T>C 2030A>C 2038A>G 2044T>A 2048A>G 2054A>C 2059A>G 2078G>C 2079C>T 2080A>G 2086T>C 2092A>T 2098T>A 2107A>C 2113T>C 2116A>G 2122A>G 2125A>G 2128A>T 2134A>T 2137A>T 2146A>C 2155G>A 2158A>G 2162C>A 2170G>A 2179T>C 2185C>G 2191T>A 2194C>T 2197A>G 2200C>T 2203G>A 2206C>T 2209A>G 2212T>C 2215A>G 2224T>C 2227T>A 2243T>A 2245A>G 2248A>C 2257T>A 2263T>A 2275A>C 2276C>T 2278T>G 2296T>G 2297T>C 2308G>T 2311A>T 2318A>G 2320A>T 2323G>A 2326T>C 2329A>G 2335G>C 2338T>A 2350T>G 2353A>G 2356A>T 2359T>C 2362A>T 2365C>A 2374A>C 2380T>A 2383C>T 2387C>T 2389T>A 2390A>C 2392A>G 2395G>A 2398C>T 2401C>T 2404G>C 2407A>G 2413C>A 2416C>A 2417C>T 2419A>G 2425G>A 2440T>G 2453T>C 2455G>A 2458G>T 2461T>C 2474A>G 2476T>G 2482A>T 2485T>A 2488T>C 2497G>A 2515A>G 2527T>C 2531G>A 2532C>A 2533G>T 2536A>G 2554T>A 2557C>T 2560A>T 2563A>T 2566T>C 2572A>T 2575T>C 2582T>C 2590G>A 2596T>A 2599A>G 2602T>C 2608T>A 2611T>A 2617A>T 2620T>A 2626T>A 2632T>A 2659A>G 2660C>T 2678T>C
CDS
1883100%568596.5%881 (99.8%)838 (94.9%)0/2/0/01
Protein mutations:
T12A (50A>G) L14I (56C>A) K15N (61A>T) Q16N (62C>A 64A>T) D17N (65G>A) E18D (70A>C) E24D (88A>T) S26E (92A>G 93G>A 94C>G) N28Q (98A>C 100C>G) I29D (101A>G 102T>A) N30Q (104A>C 106T>A) D32N (110G>A 112C>T) S33_P34del (113_118delAGTCCT) K35R (120A>G) S36M (122T>A 123C>T 124A>G) E40D (136A>C) I49V (161A>G 163A>C) I50V (164A>G 166T>A) V57I (185G>A) S60A (194T>G) N67T (216A>C 217T>G) V88I (278G>A 280T>A) K131R (408A>G) R142K (441G>A) R154K (476C>A 477G>A 478A>G) M177T (546T>C 547G>T) A208S (638G>A 639C>G 640A>T) H252Y (770C>T 772T>C) I416V (1262A>G 1264T>G) I434V (1316A>G 1318A>G) V438I (1328G>A 1330T>A) Y479N (1451T>A 1453T>C) V505I (1529G>A 1531C>T) S553A (1673T>G 1675A>T) I563V (1703A>G 1705A>T) S642A (1940T>G) Q652H (1972G>C) I678V (2048A>G) A688L (2078G>C 2079C>T 2080A>G) E692D (2092A>T) S743T (2243T>A 2245A>G) I768V (2318A>G 2320A>T) I820V (2474A>G 2476T>G) A839N (2531G>A 2532C>A 2533G>T)
Codon mutations:
TAT3TAC (25T>C) CGA4AGG (26C>A 28A>G) CGT9CGC (43T>C) ACG12GCG (50A>G) CTA14ATA (56C>A) AAA15AAT (61A>T) CAA16AAT (62C>A 64A>T) GAT17AAT (65G>A) GAA18GAC (70A>C) GAA22GAG (82A>G) GAA24GAT (88A>T) GAT25GAC (91T>C) AGC26GAG (92A>G 93G>A 94C>G) AAC28CAG (98A>C 100C>G) ATT29GAT (101A>G 102T>A) AAT30CAA (104A>C 106T>A) AAT31AAC (109T>C) GAC32AAT (110G>A 112C>T) AGT33_CCT34del (113_118delAGTCCT) AAA35AGA (120A>G) TCA36ATG (122T>A 123C>T 124A>G) TCA39TCT (133A>T) GAA40GAC (136A>C) TTA43CTT (143T>C 145A>T) TCT44TCA (148T>A) GAA47GAG (157A>G) GAG48GAA (160G>A) ATA49GTC (161A>G 163A>C) ATT50GTA (164A>G 166T>A) ACA51ACC (169A>C) GAT52GAC (172T>C) GAA55GAG (181A>G) GTT57ATT (185G>A) ATA59ATT (193A>T) TCT60GCT (194T>G) GAG62GAA (202G>A) GTA63GTG (205A>G) AAA64AAG (208A>G) TCT66TCA (214T>A) AAT67ACG (216A>C 217T>G) TCG71TCT (229G>T) CAG73CAA (235G>A) TTA75CTT (239T>C 241A>T) GTA77GTT (247A>T) CTT78TTG (248C>T 250T>G) GAG82GAA (262G>A) GAA83GAG (265A>G) CAT84CAC (268T>C) GTT88ATA (278G>A 280T>A) ATA92ATT (292A>T) ACT96ACG (304T>G) ATC97ATA (307C>A) CCT98CCA (310T>A) CTC107TTG (335C>T 337C>G) AAA108AAG (340A>G) TTA110TTG (346A>G) GAC112GAT (352C>T) ATA113ATC (355A>C) CCA115CCG (361A>G) CAA117CAG (367A>G) GCA118GCG (370A>G) AAA120AAG (376A>G) CAA121CAG (379A>G) AAA123AAG (385A>G) CTG124CTA (388G>A) CGA126AGA (392C>A) AAA131AGA (408A>G) CAA132CAG (412A>G) TTG133CTG (413T>C) CCT134CCA (418T>A) GCT138GCA (430T>A) GGA140GGT (436A>T) AGA142AAA (441G>A) CTT144TTG (446C>T 448T>G) AAT146AAC (454T>C) AAA151AAG (469A>G) AAA153AAG (475A>G) CGA154AAG (476C>A 477G>A 478A>G) CTT157TTA (485C>T 487T>A) CCT158CCA (490T>A) GAT163GAC (505T>C) TTA169CTA (521T>C) TTA171TTG (529A>G) CAA174CAG (538A>G) GTA175GTT (541A>T) TTA176CTT (542T>C 544A>T) ATG177ACT (546T>C 547G>T) CCG180CCA (556G>A) CTA183TTA (563C>T) TTA184CTA (566T>C) CTT185TTA (569C>T 571T>A) GCT189GCA (583T>A) GTA190GTT (586A>T) GAG191GAA (589G>A) AAT194AAC (598T>C) AGG196AGA (604G>A) GGC199GGT (613C>T) GTA201GTT (619A>T) GTT202GTC (622T>C) ACA206ACG (634A>G) GCC207GCA (637C>A) GCA208AGT (638G>A 639C>G 640A>T) ATA209ATC (643A>C) TGC210TGT (646C>T) ATT213ATA (655T>A) GAA217GAG (667A>G) ACC219ACA (673C>A) GGT221GGC (679T>C) GTA223GTG (685A>G) ATA227ATT (697A>T) GCT228GCG (700T>G) CGA233CGC (715A>C) GTT234GTA (718T>A) GAT237GAC (727T>C) CGA238AGG (728C>A 730A>G) AAT239AAC (733T>C) GTA240GTT (736A>T) TAT243TAC (745T>C) TCT245TCA (751T>A) TTG247TTA (757G>A) ATT250ATA (766T>A) GAC251GAT (769C>T) CAT252TAC (770C>T 772T>C) GCG253GCT (775G>T) TTT254TTC (778T>C) AAC255AAT (781C>T) GAA256GAG (784A>G) TAC257TAT (787C>T) TTC258TTT (790C>T) CAG262CAA (802G>A) TTG263TTA (805G>A) GTA264GTT (808A>T) ATC271ATA (829C>A) ATT272ATA (832T>A) ATA276ATT (844A>T) CCA277CCT (847A>T) GAG278GAA (850G>A) AGA279AGG (853A>G) AGA281AGG (859A>G) GAT283GAC (865T>C) GTC284GTT (868C>T) TTA288CTT (878T>C 880A>T) AGG292AGA (892G>A) TTA294CTG (896T>C 898A>G) CCG295CCA (901G>A) TCT296TCA (904T>A) ACT297ACA (907T>A) ATC301ATA (919C>A) CCA303CCT (925A>T) AAC304AAT (928C>T) TTG305TTA (931G>A) GAT308GAC (940T>C) AGG309AGA (943G>A) TTA310CTG (944T>C 946A>G) TTA312TTG (952A>G) CAT313CAC (955T>C) GAG317GAA (967G>A) TCA318TCC (970A>C) CTC319TTG (971C>T 973C>G) ACT322ACG (982T>G) ACT324ACA (988T>A) ACA325ACT (991A>T) TCT326TCA (994T>A) AAT327AAC (997T>C) TTA330CTG (1004T>C 1006A>G) TCT333TCG (1015T>G) GTG334GTA (1018G>A) GTG335GTA (1021G>A) CCA336CCG (1024A>G) GAC337GAT (1027C>T) CTA338TTA (1028C>T) AAA339AAG (1033A>G) GTA342GTT (1042A>T) TCT343TCA (1045T>A) ACT344ACC (1048T>C) GAG345GAA (1051G>A) GCA346GCG (1054A>G) ATC348ATT (1060C>T) CAG349CAA (1063G>A) TCA352TCG (1072A>G) TTG357CTA (1085T>C 1087G>A) GCT359GCA (1093T>A) TTG360TTA (1096G>A) CAA363CAG (1105A>G) GAG365GAA (1111G>A) ACT366ACG (1114T>G) GCC376GCG (1144C>G) GCT377GCA (1147T>A) GAT379GAC (1153T>C) TTT381TTC (1159T>C) TTG384CTG (1166T>C) GCT386GCA (1174T>A) GCT387GCA (1177T>A) TTG389TTA (1183G>A) CAG391CAA (1189G>A) TCA395TCG (1201A>G) TTA396CTT (1202T>C 1204A>T) GTA399GTG (1213A>G) ACG400ACT (1216G>T) TAC403TAT (1225C>T) CTT406TTA (1232C>T 1234T>A) GGC409GGT (1243C>T) CTC413CTA (1255C>A) GTG415GTA (1261G>A) ATT416GTG (1262A>G 1264T>G) GAT419GAC (1273T>C) TTT421TTC (1279T>C) AGA423AGG (1285A>G) TTA426TTG (1294A>G) GTA427GTT (1297A>T) TGT429TGC (1303T>C) CTA431CTG (1309A>G) GCC432GCT (1312C>T) ATA434GTG (1316A>G 1318A>G) ACC436ACA (1324C>A) ATT437ATA (1327T>A) GTT438ATA (1328G>A 1330T>A) CCG440CCA (1336G>A) GCA441GCG (1339A>G) AGA446CGA (1352A>C) AGG450AGA (1366G>A) AAT451AAC (1369T>C) GGT452GGA (1372T>A) ACT456ACA (1384T>A) CCC457CCA (1387C>A) CAA459CAG (1393A>G) ATT460ATA (1396T>A) GAG462GAA (1402G>A) CAA463CAG (1405A>G) ATT465ATA (1411T>A) TTT468TTC (1420T>C) GCT471GCG (1429T>G) TTA474CTG (1436T>C 1438A>G) GTT477GTC (1447T>C) TAT479AAC (1451T>A 1453T>C) CAG481CAA (1459G>A) GTG486GTT (1474G>T) GGA489GGT (1483A>T) GTG490GTA (1486G>A) TTA491TTG (1489A>G) CAA493CAG (1495A>G) GTC494GTA (1498C>A) TTG495CTG (1499T>C) GAT497GAC (1507T>C) ATA499ATT (1513A>T) GGT502GGA (1522T>A) GTA504GTC (1528A>C) GTC505ATT (1529G>A 1531C>T) AAC506AAT (1534C>T) CAA507CAG (1537A>G) TTA508TTG (1540A>G) GAA510GAG (1546A>G) CTG512TTA (1550C>T 1552G>A) TTA515CTA (1559T>C) TCT516TCA (1564T>A) AGA517CGA (1565A>C) CCC521CCA (1579C>A) CCA524CCT (1588A>T) AAA528AAG (1600A>G) AGA529AGG (1603A>G) TCT530TCA (1606T>A) ATA531ATC (1609A>C) AGA533CGT (1613A>C 1615A>T) ATT535ATA (1621T>A) TTG536TTA (1624G>A) CTG537TTG (1625C>T) CTT538CTA (1630T>A) TCT539TCA (1633T>A) AAC540AAT (1636C>T) AGA541AGG (1639A>G) CAG544CAA (1648G>A) CTT545TTA (1649C>T 1651T>A) GTC546GTT (1654C>T) ACA549ACT (1663A>T) AGA550AGG (1666A>G) TTG551TTA (1669G>A) TCA553GCT (1673T>G 1675A>T) AAT555AAC (1681T>C) TAT556TAC (1684T>C) GAG557GAA (1687G>A) TTA559CTA (1691T>C) TGC562TGT (1702C>T) ATA563GTT (1703A>G 1705A>T) ACA564ACG (1708A>G) CAG568CAA (1720G>A) CAA571CAG (1729A>G) ACA572ACT (1732A>T) TTA573TTG (1735A>G) ACT575ACA (1741T>A) TTG578TTA (1750G>A) CAA579CAG (1753A>G) ACA581ACT (1759A>T) GTA583GTC (1765A>C) ACA584ACG (1768A>G) TCA585TCG (1771A>G) TTA586TTG (1774A>G) CTA589CTT (1783A>T) GGA591GGT (1789A>T) GCT593GCA (1795T>A) ACG594ACC (1798G>C) CCG597CCC (1807G>C) AGT598AGC (1810T>C) CAA600CAG (1816A>G) TTG602TTA (1822G>A) TTC603TTT (1825C>T) CAT604CAC (1828T>C) TAC605TAT (1831C>T) GTG608GTT (1840G>T) GTC610GTT (1846C>T) GAC622GAT (1882C>T) GTT624GTG (1888T>G) GCA625GCC (1891A>C) ATT626ATA (1894T>A) GCG629GCA (1903G>A) GCA630GCT (1906A>T) TTA633CTA (1913T>C) CAA637CAG (1927A>G) AAG638AAA (1930G>A) AAA639AAG (1933A>G) AAA641AAG (1939A>G) TCA642GCA (1940T>G) GAG645GAA (1951G>A) GAC646GAT (1954C>T) CTG648TTA (1958C>T 1960G>A) CAG652CAC (1972G>C) ATA653ATT (1975A>T) TTT654TTC (1978T>C) GTT656GTA (1984T>A) GCG657GCT (1987G>T) GTA659GTT (1993A>T) GAC662GAT (2002C>T) TTG667TTA (2017G>A) AGA668AGG (2020A>G) TTA671CTA (2027T>C) AGA672CGA (2030A>C) TTA674TTG (2038A>G) GTT676GTA (2044T>A) ATA678GTA (2048A>G) AGA680CGA (2054A>C) TTA681TTG (2059A>G) GCA688CTG (2078G>C 2079C>T 2080A>G) AAT690AAC (2086T>C) GAA692GAT (2092A>T) ATT694ATA (2098T>A) GCA697GCC (2107A>C) GAT699GAC (2113T>C) AAA700AAG (2116A>G) GCA702GCG (2122A>G) CAA703CAG (2125A>G) GGA704GGT (2128A>T) ATA706ATT (2134A>T) ATA707ATT (2137A>T) CGA710CGC (2146A>C) CAG713CAA (2155G>A) TTA714TTG (2158A>G) CGA716AGA (2162C>A) GAG718GAA (2170G>A) GGT721GGC (2179T>C) GTC723GTG (2185C>G) ATT725ATA (2191T>A) GCC726GCT (2194C>T) AGA727AGG (2197A>G) AAC728AAT (2200C>T) TTG729TTA (2203G>A) GAC730GAT (2206C>T) GGA731GGG (2209A>G) TTT732TTC (2212T>C) CAA733CAG (2215A>G) AAT736AAC (2224T>C) CTT737CTA (2227T>A) TCA743ACG (2243T>A 2245A>G) GGA744GGC (2248A>C) GCT747GCA (2257T>A) ATT749ATA (2263T>A) CTA753CTC (2275A>C) CTT754TTG (2276C>T 2278T>G) GCT760GCG (2296T>G) TTA761CTA (2297T>C) GCG764GCT (2308G>T) CTA765CTT (2311A>T) ATA768GTT (2318A>G 2320A>T) ACG769ACA (2323G>A) GAT770GAC (2326T>C) TCA771TCG (2329A>G) GTG773GTC (2335G>C) ATT774ATA (2338T>A) GCT778GCG (2350T>G) AAA779AAG (2353A>G) CTA780CTT (2356A>T) GAT781GAC (2359T>C) GCA782GCT (2362A>T) ACC783ACA (2365C>A) GCA786GCC (2374A>C) ATT788ATA (2380T>A) GTC789GTT (2383C>T) CTT791TTA (2387C>T 2389T>A) AGA792CGG (2390A>C 2392A>G) AAG793AAA (2395G>A) GTC794GTT (2398C>T) GAC795GAT (2401C>T) ACG796ACC (2404G>C) TTA797TTG (2407A>G) CCC799CCA (2413C>A) ATC800ATA (2416C>A) CTA801TTG (2417C>T 2419A>G) AAG803AAA (2425G>A) TCT808TCG (2440T>G) TTG813CTA (2453T>C 2455G>A) GTG814GTT (2458G>T) GCT815GCC (2461T>C) ATT820GTG (2474A>G 2476T>G) ACA822ACT (2482A>T) TCT823TCA (2485T>A) ACT824ACC (2488T>C) GTG827GTA (2497G>A) CAA833CAG (2515A>G) TTT837TTC (2527T>C) GCG839AAT (2531G>A 2532C>A 2533G>T) TCA840TCG (2536A>G) TCT846TCA (2554T>A) AAC847AAT (2557C>T) CTA848CTT (2560A>T) ACA849ACT (2563A>T) TTT850TTC (2566T>C) GTA852GTT (2572A>T) TAT853TAC (2575T>C) TTG856CTG (2582T>C) GCG858GCA (2590G>A) GTT860GTA (2596T>A) TCA861TCG (2599A>G) GCT862GCC (2602T>C) ACT864ACA (2608T>A) GTT865GTA (2611T>A) CCA867CCT (2617A>T) ATT868ATA (2620T>A) GCT870GCA (2626T>A) GCT872GCA (2632T>A) GAA881GAG (2659A>G) CTG882TTG (2660C>T)
Proteins
1883100%568596.5%881 (99.8%)838 (94.9%)0/2/0/01
Protein mutations:
T12A (50A>G) L14I (56C>A) K15N (61A>T) Q16N (62C>A 64A>T) D17N (65G>A) E18D (70A>C) E24D (88A>T) S26E (92A>G 93G>A 94C>G) N28Q (98A>C 100C>G) I29D (101A>G 102T>A) N30Q (104A>C 106T>A) D32N (110G>A 112C>T) S33_P34del (113_118delAGTCCT) K35R (120A>G) S36M (122T>A 123C>T 124A>G) E40D (136A>C) I49V (161A>G 163A>C) I50V (164A>G 166T>A) V57I (185G>A) S60A (194T>G) N67T (216A>C 217T>G) V88I (278G>A 280T>A) K131R (408A>G) R142K (441G>A) R154K (476C>A 477G>A 478A>G) M177T (546T>C 547G>T) A208S (638G>A 639C>G 640A>T) H252Y (770C>T 772T>C) I416V (1262A>G 1264T>G) I434V (1316A>G 1318A>G) V438I (1328G>A 1330T>A) Y479N (1451T>A 1453T>C) V505I (1529G>A 1531C>T) S553A (1673T>G 1675A>T) I563V (1703A>G 1705A>T) S642A (1940T>G) Q652H (1972G>C) I678V (2048A>G) A688L (2078G>C 2079C>T 2080A>G) E692D (2092A>T) S743T (2243T>A 2245A>G) I768V (2318A>G 2320A>T) I820V (2474A>G 2476T>G) A839N (2531G>A 2532C>A 2533G>T)
Codon mutations:
TAT3TAC (25T>C) CGA4AGG (26C>A 28A>G) CGT9CGC (43T>C) ACG12GCG (50A>G) CTA14ATA (56C>A) AAA15AAT (61A>T) CAA16AAT (62C>A 64A>T) GAT17AAT (65G>A) GAA18GAC (70A>C) GAA22GAG (82A>G) GAA24GAT (88A>T) GAT25GAC (91T>C) AGC26GAG (92A>G 93G>A 94C>G) AAC28CAG (98A>C 100C>G) ATT29GAT (101A>G 102T>A) AAT30CAA (104A>C 106T>A) AAT31AAC (109T>C) GAC32AAT (110G>A 112C>T) AGT33_CCT34del (113_118delAGTCCT) AAA35AGA (120A>G) TCA36ATG (122T>A 123C>T 124A>G) TCA39TCT (133A>T) GAA40GAC (136A>C) TTA43CTT (143T>C 145A>T) TCT44TCA (148T>A) GAA47GAG (157A>G) GAG48GAA (160G>A) ATA49GTC (161A>G 163A>C) ATT50GTA (164A>G 166T>A) ACA51ACC (169A>C) GAT52GAC (172T>C) GAA55GAG (181A>G) GTT57ATT (185G>A) ATA59ATT (193A>T) TCT60GCT (194T>G) GAG62GAA (202G>A) GTA63GTG (205A>G) AAA64AAG (208A>G) TCT66TCA (214T>A) AAT67ACG (216A>C 217T>G) TCG71TCT (229G>T) CAG73CAA (235G>A) TTA75CTT (239T>C 241A>T) GTA77GTT (247A>T) CTT78TTG (248C>T 250T>G) GAG82GAA (262G>A) GAA83GAG (265A>G) CAT84CAC (268T>C) GTT88ATA (278G>A 280T>A) ATA92ATT (292A>T) ACT96ACG (304T>G) ATC97ATA (307C>A) CCT98CCA (310T>A) CTC107TTG (335C>T 337C>G) AAA108AAG (340A>G) TTA110TTG (346A>G) GAC112GAT (352C>T) ATA113ATC (355A>C) CCA115CCG (361A>G) CAA117CAG (367A>G) GCA118GCG (370A>G) AAA120AAG (376A>G) CAA121CAG (379A>G) AAA123AAG (385A>G) CTG124CTA (388G>A) CGA126AGA (392C>A) AAA131AGA (408A>G) CAA132CAG (412A>G) TTG133CTG (413T>C) CCT134CCA (418T>A) GCT138GCA (430T>A) GGA140GGT (436A>T) AGA142AAA (441G>A) CTT144TTG (446C>T 448T>G) AAT146AAC (454T>C) AAA151AAG (469A>G) AAA153AAG (475A>G) CGA154AAG (476C>A 477G>A 478A>G) CTT157TTA (485C>T 487T>A) CCT158CCA (490T>A) GAT163GAC (505T>C) TTA169CTA (521T>C) TTA171TTG (529A>G) CAA174CAG (538A>G) GTA175GTT (541A>T) TTA176CTT (542T>C 544A>T) ATG177ACT (546T>C 547G>T) CCG180CCA (556G>A) CTA183TTA (563C>T) TTA184CTA (566T>C) CTT185TTA (569C>T 571T>A) GCT189GCA (583T>A) GTA190GTT (586A>T) GAG191GAA (589G>A) AAT194AAC (598T>C) AGG196AGA (604G>A) GGC199GGT (613C>T) GTA201GTT (619A>T) GTT202GTC (622T>C) ACA206ACG (634A>G) GCC207GCA (637C>A) GCA208AGT (638G>A 639C>G 640A>T) ATA209ATC (643A>C) TGC210TGT (646C>T) ATT213ATA (655T>A) GAA217GAG (667A>G) ACC219ACA (673C>A) GGT221GGC (679T>C) GTA223GTG (685A>G) ATA227ATT (697A>T) GCT228GCG (700T>G) CGA233CGC (715A>C) GTT234GTA (718T>A) GAT237GAC (727T>C) CGA238AGG (728C>A 730A>G) AAT239AAC (733T>C) GTA240GTT (736A>T) TAT243TAC (745T>C) TCT245TCA (751T>A) TTG247TTA (757G>A) ATT250ATA (766T>A) GAC251GAT (769C>T) CAT252TAC (770C>T 772T>C) GCG253GCT (775G>T) TTT254TTC (778T>C) AAC255AAT (781C>T) GAA256GAG (784A>G) TAC257TAT (787C>T) TTC258TTT (790C>T) CAG262CAA (802G>A) TTG263TTA (805G>A) GTA264GTT (808A>T) ATC271ATA (829C>A) ATT272ATA (832T>A) ATA276ATT (844A>T) CCA277CCT (847A>T) GAG278GAA (850G>A) AGA279AGG (853A>G) AGA281AGG (859A>G) GAT283GAC (865T>C) GTC284GTT (868C>T) TTA288CTT (878T>C 880A>T) AGG292AGA (892G>A) TTA294CTG (896T>C 898A>G) CCG295CCA (901G>A) TCT296TCA (904T>A) ACT297ACA (907T>A) ATC301ATA (919C>A) CCA303CCT (925A>T) AAC304AAT (928C>T) TTG305TTA (931G>A) GAT308GAC (940T>C) AGG309AGA (943G>A) TTA310CTG (944T>C 946A>G) TTA312TTG (952A>G) CAT313CAC (955T>C) GAG317GAA (967G>A) TCA318TCC (970A>C) CTC319TTG (971C>T 973C>G) ACT322ACG (982T>G) ACT324ACA (988T>A) ACA325ACT (991A>T) TCT326TCA (994T>A) AAT327AAC (997T>C) TTA330CTG (1004T>C 1006A>G) TCT333TCG (1015T>G) GTG334GTA (1018G>A) GTG335GTA (1021G>A) CCA336CCG (1024A>G) GAC337GAT (1027C>T) CTA338TTA (1028C>T) AAA339AAG (1033A>G) GTA342GTT (1042A>T) TCT343TCA (1045T>A) ACT344ACC (1048T>C) GAG345GAA (1051G>A) GCA346GCG (1054A>G) ATC348ATT (1060C>T) CAG349CAA (1063G>A) TCA352TCG (1072A>G) TTG357CTA (1085T>C 1087G>A) GCT359GCA (1093T>A) TTG360TTA (1096G>A) CAA363CAG (1105A>G) GAG365GAA (1111G>A) ACT366ACG (1114T>G) GCC376GCG (1144C>G) GCT377GCA (1147T>A) GAT379GAC (1153T>C) TTT381TTC (1159T>C) TTG384CTG (1166T>C) GCT386GCA (1174T>A) GCT387GCA (1177T>A) TTG389TTA (1183G>A) CAG391CAA (1189G>A) TCA395TCG (1201A>G) TTA396CTT (1202T>C 1204A>T) GTA399GTG (1213A>G) ACG400ACT (1216G>T) TAC403TAT (1225C>T) CTT406TTA (1232C>T 1234T>A) GGC409GGT (1243C>T) CTC413CTA (1255C>A) GTG415GTA (1261G>A) ATT416GTG (1262A>G 1264T>G) GAT419GAC (1273T>C) TTT421TTC (1279T>C) AGA423AGG (1285A>G) TTA426TTG (1294A>G) GTA427GTT (1297A>T) TGT429TGC (1303T>C) CTA431CTG (1309A>G) GCC432GCT (1312C>T) ATA434GTG (1316A>G 1318A>G) ACC436ACA (1324C>A) ATT437ATA (1327T>A) GTT438ATA (1328G>A 1330T>A) CCG440CCA (1336G>A) GCA441GCG (1339A>G) AGA446CGA (1352A>C) AGG450AGA (1366G>A) AAT451AAC (1369T>C) GGT452GGA (1372T>A) ACT456ACA (1384T>A) CCC457CCA (1387C>A) CAA459CAG (1393A>G) ATT460ATA (1396T>A) GAG462GAA (1402G>A) CAA463CAG (1405A>G) ATT465ATA (1411T>A) TTT468TTC (1420T>C) GCT471GCG (1429T>G) TTA474CTG (1436T>C 1438A>G) GTT477GTC (1447T>C) TAT479AAC (1451T>A 1453T>C) CAG481CAA (1459G>A) GTG486GTT (1474G>T) GGA489GGT (1483A>T) GTG490GTA (1486G>A) TTA491TTG (1489A>G) CAA493CAG (1495A>G) GTC494GTA (1498C>A) TTG495CTG (1499T>C) GAT497GAC (1507T>C) ATA499ATT (1513A>T) GGT502GGA (1522T>A) GTA504GTC (1528A>C) GTC505ATT (1529G>A 1531C>T) AAC506AAT (1534C>T) CAA507CAG (1537A>G) TTA508TTG (1540A>G) GAA510GAG (1546A>G) CTG512TTA (1550C>T 1552G>A) TTA515CTA (1559T>C) TCT516TCA (1564T>A) AGA517CGA (1565A>C) CCC521CCA (1579C>A) CCA524CCT (1588A>T) AAA528AAG (1600A>G) AGA529AGG (1603A>G) TCT530TCA (1606T>A) ATA531ATC (1609A>C) AGA533CGT (1613A>C 1615A>T) ATT535ATA (1621T>A) TTG536TTA (1624G>A) CTG537TTG (1625C>T) CTT538CTA (1630T>A) TCT539TCA (1633T>A) AAC540AAT (1636C>T) AGA541AGG (1639A>G) CAG544CAA (1648G>A) CTT545TTA (1649C>T 1651T>A) GTC546GTT (1654C>T) ACA549ACT (1663A>T) AGA550AGG (1666A>G) TTG551TTA (1669G>A) TCA553GCT (1673T>G 1675A>T) AAT555AAC (1681T>C) TAT556TAC (1684T>C) GAG557GAA (1687G>A) TTA559CTA (1691T>C) TGC562TGT (1702C>T) ATA563GTT (1703A>G 1705A>T) ACA564ACG (1708A>G) CAG568CAA (1720G>A) CAA571CAG (1729A>G) ACA572ACT (1732A>T) TTA573TTG (1735A>G) ACT575ACA (1741T>A) TTG578TTA (1750G>A) CAA579CAG (1753A>G) ACA581ACT (1759A>T) GTA583GTC (1765A>C) ACA584ACG (1768A>G) TCA585TCG (1771A>G) TTA586TTG (1774A>G) CTA589CTT (1783A>T) GGA591GGT (1789A>T) GCT593GCA (1795T>A) ACG594ACC (1798G>C) CCG597CCC (1807G>C) AGT598AGC (1810T>C) CAA600CAG (1816A>G) TTG602TTA (1822G>A) TTC603TTT (1825C>T) CAT604CAC (1828T>C) TAC605TAT (1831C>T) GTG608GTT (1840G>T) GTC610GTT (1846C>T) GAC622GAT (1882C>T) GTT624GTG (1888T>G) GCA625GCC (1891A>C) ATT626ATA (1894T>A) GCG629GCA (1903G>A) GCA630GCT (1906A>T) TTA633CTA (1913T>C) CAA637CAG (1927A>G) AAG638AAA (1930G>A) AAA639AAG (1933A>G) AAA641AAG (1939A>G) TCA642GCA (1940T>G) GAG645GAA (1951G>A) GAC646GAT (1954C>T) CTG648TTA (1958C>T 1960G>A) CAG652CAC (1972G>C) ATA653ATT (1975A>T) TTT654TTC (1978T>C) GTT656GTA (1984T>A) GCG657GCT (1987G>T) GTA659GTT (1993A>T) GAC662GAT (2002C>T) TTG667TTA (2017G>A) AGA668AGG (2020A>G) TTA671CTA (2027T>C) AGA672CGA (2030A>C) TTA674TTG (2038A>G) GTT676GTA (2044T>A) ATA678GTA (2048A>G) AGA680CGA (2054A>C) TTA681TTG (2059A>G) GCA688CTG (2078G>C 2079C>T 2080A>G) AAT690AAC (2086T>C) GAA692GAT (2092A>T) ATT694ATA (2098T>A) GCA697GCC (2107A>C) GAT699GAC (2113T>C) AAA700AAG (2116A>G) GCA702GCG (2122A>G) CAA703CAG (2125A>G) GGA704GGT (2128A>T) ATA706ATT (2134A>T) ATA707ATT (2137A>T) CGA710CGC (2146A>C) CAG713CAA (2155G>A) TTA714TTG (2158A>G) CGA716AGA (2162C>A) GAG718GAA (2170G>A) GGT721GGC (2179T>C) GTC723GTG (2185C>G) ATT725ATA (2191T>A) GCC726GCT (2194C>T) AGA727AGG (2197A>G) AAC728AAT (2200C>T) TTG729TTA (2203G>A) GAC730GAT (2206C>T) GGA731GGG (2209A>G) TTT732TTC (2212T>C) CAA733CAG (2215A>G) AAT736AAC (2224T>C) CTT737CTA (2227T>A) TCA743ACG (2243T>A 2245A>G) GGA744GGC (2248A>C) GCT747GCA (2257T>A) ATT749ATA (2263T>A) CTA753CTC (2275A>C) CTT754TTG (2276C>T 2278T>G) GCT760GCG (2296T>G) TTA761CTA (2297T>C) GCG764GCT (2308G>T) CTA765CTT (2311A>T) ATA768GTT (2318A>G 2320A>T) ACG769ACA (2323G>A) GAT770GAC (2326T>C) TCA771TCG (2329A>G) GTG773GTC (2335G>C) ATT774ATA (2338T>A) GCT778GCG (2350T>G) AAA779AAG (2353A>G) CTA780CTT (2356A>T) GAT781GAC (2359T>C) GCA782GCT (2362A>T) ACC783ACA (2365C>A) GCA786GCC (2374A>C) ATT788ATA (2380T>A) GTC789GTT (2383C>T) CTT791TTA (2387C>T 2389T>A) AGA792CGG (2390A>C 2392A>G) AAG793AAA (2395G>A) GTC794GTT (2398C>T) GAC795GAT (2401C>T) ACG796ACC (2404G>C) TTA797TTG (2407A>G) CCC799CCA (2413C>A) ATC800ATA (2416C>A) CTA801TTG (2417C>T 2419A>G) AAG803AAA (2425G>A) TCT808TCG (2440T>G) TTG813CTA (2453T>C 2455G>A) GTG814GTT (2458G>T) GCT815GCC (2461T>C) ATT820GTG (2474A>G 2476T>G) ACA822ACT (2482A>T) TCT823TCA (2485T>A) ACT824ACC (2488T>C) GTG827GTA (2497G>A) CAA833CAG (2515A>G) TTT837TTC (2527T>C) GCG839AAT (2531G>A 2532C>A 2533G>T) TCA840TCG (2536A>G) TCT846TCA (2554T>A) AAC847AAT (2557C>T) CTA848CTT (2560A>T) ACA849ACT (2563A>T) TTT850TTC (2566T>C) GTA852GTT (2572A>T) TAT853TAC (2575T>C) TTG856CTG (2582T>C) GCG858GCA (2590G>A) GTT860GTA (2596T>A) TCA861TCG (2599A>G) GCT862GCC (2602T>C) ACT864ACA (2608T>A) GTT865GTA (2611T>A) CCA867CCT (2617A>T) ATT868ATA (2620T>A) GCT870GCA (2626T>A) GCT872GCA (2632T>A) GAA881GAG (2659A>G) CTG882TTG (2660C>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43