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Merge pull request #182 from MarieLataretu/master
added V4.1 fixes #175
2 parents 55acad7 + a147e2c commit c53af98

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‎README.md

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* poreCov was coded with "easy to use" in mind, while staying flexible
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* therefore we provide a few input types which adjusts the workflow automatically (see image below)
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* fast5 raw data, fastq files (one sample per file), fastq_pass (the basecalling output) or fasta (supports multifastas)
178-
* primer schemes for ARTIC can be V1, V2, V3(default) or V1200 (the 1200bp amplicon ones)
178+
* primer schemes for ARTIC can be V1, V2, V3(default), V4, V4.1 or V1200 (the 1200bp amplicon ones)
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<p align="left">
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<img src="data/figures/workflow.png" width="700" title="Workflow">

‎data/external_primer_schemes/nCoV-2019/V4.1/README.md

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https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342

‎data/external_primer_schemes/nCoV-2019/V4.1/nCoV-2019.primer.bed

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1+
MN908947.3 25 50 SARS-CoV-2_1_LEFT 1 + AACAAACCAACCAACTTTCGATCTC
2+
MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - CTTCTACTAAGCCACAAGTGCCA
3+
MN908947.3 324 344 SARS-CoV-2_2_LEFT 2 + TTTACAGGTTCGCGACGTGC
4+
MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - ATAAGGATCAGTGCCAAGCTCG
5+
MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + GTAATAAAGGAGCTGGTGGCCA
6+
MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - GCCAATTTAATTTCAAAAGGTGTCTGC
7+
MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + GTGTATACTGCTGCCGTGAACA
8+
MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - ACAACAGCATTTTGGGGTAAGTAAC
9+
MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + TGAAACTTCATGGCAGACGGG
10+
MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - TTGATGTTGACTTTCTCTTTTTGGAGT
11+
MN908947.3 1540 1562 SARS-CoV-2_6_LEFT 2 + CGTGCTAGCGCTAACATAGGTT
12+
MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT 2 - AACACGCACAGAATTTTGAGCAG
13+
MN908947.3 1851 1875 SARS-CoV-2_7_LEFT 1 + ACTGAGTCCTCTTTATGCATTTGC
14+
MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT 1 - CCACCGACAATTTCACAAGCAC
15+
MN908947.3 2154 2180 SARS-CoV-2_8_LEFT 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG
16+
MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT 2 - GGTTGTTCTAATGGTTGTAAATCACCA
17+
MN908947.3 2483 2508 SARS-CoV-2_9_LEFT 1 + TCTTCTTAGAGGGAGAAACACTTCC
18+
MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT 1 - CACAGGCGAACTCATTTACTTCTG
19+
MN908947.3 2826 2850 SARS-CoV-2_10_LEFT 2 + TGAGAAGTGCTCTGCCTATACAGT
20+
MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT 2 - TCATCTAACCAATCTTCTTCTTGCTCT
21+
MN908947.3 3078 3102 SARS-CoV-2_11_LEFT 1 + AGAAGAGTTTGAGCCATCAACTCA
22+
MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT 1 - TTTAAGGCTCCTGCAACACCTC
23+
MN908947.3 3390 3412 SARS-CoV-2_12_LEFT 2 + TGCAGACATTGTGGAAGAAGCT
24+
MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT 2 - CAGCTAAGTAGACATTTGTGCGAAC
25+
MN908947.3 3683 3705 SARS-CoV-2_13_LEFT 1 + AGCACGAAGTTCTACTTGCACC
26+
MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT 1 - GATGTCAATGTCACTAACAAGAGTGG
27+
MN908947.3 3992 4018 SARS-CoV-2_14_LEFT 2 + TGGAAGAAACTAAGTTCCTCACAGAA
28+
MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT 2 - CATGTGCAAGCATTTCTCGCAA
29+
MN908947.3 4312 4339 SARS-CoV-2_15_LEFT 1 + AAAAGTGCCTTTTACATTCTACCATCT
30+
MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT 1 - GCATCAGGTGAAGAAACAGAAACTG
31+
MN908947.3 4620 4648 SARS-CoV-2_16_LEFT 2 + TGTAACACATGGCTTAAATTTGGAAGAA
32+
MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT 2 - CACAACTTGCGTGTGGAGGTTA
33+
MN908947.3 4923 4953 SARS-CoV-2_17_LEFT 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG
34+
MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA
35+
MN908947.3 5230 5259 SARS-CoV-2_18_LEFT 2 + TGGAAATACCCACAAGTTAATGGTTTAAC
36+
MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT 2 - GCTTGTTTACCACACGTACAAGG
37+
MN908947.3 5561 5584 SARS-CoV-2_19_LEFT 1 + AAGCTGTTATGTACATGGGCACA
38+
MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT 1 - TGTCCAACTTAGGGTCAATTTCTGT
39+
MN908947.3 5867 5894 SARS-CoV-2_20_LEFT 2 + ACAAAGAAAACAGTTACACAACAACCA
40+
MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT 2 - ACGTGGCTTTATTAGTTGCATTGTT
41+
MN908947.3 6184 6210 SARS-CoV-2_21_LEFT 1 + CACTACACACCCTCTTTTAAGAAAGG
42+
MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT 1 - GTAAGACTAGAATTGTCTACATAAGCAGC
43+
MN908947.3 6478 6507 SARS-CoV-2_22_LEFT 2 + GTAGGAGACATTATACTTAAACCAGCAAA
44+
MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT 2 - CCGACACTCTTAACAGTATTCTTTGC
45+
MN908947.3 6747 6776 SARS-CoV-2_23_LEFT 1 + AAACCGTGTTTGTACTAATTATATGCCTT
46+
MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT 1 - AACCACTAAGACAAACACTACAAGGT
47+
MN908947.3 7057 7084 SARS-CoV-2_24_LEFT 2 + GGTTACAGAGAAGGCTATTTGAACTCT
48+
MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT 2 - ACAACATGCACATAACTTTTCCATACA
49+
MN908947.3 7381 7403 SARS-CoV-2_25_LEFT 1 + CAAATGGCCCCGATTTCAGCTA
50+
MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT 1 - TGGATGGAACCATTCTTCACTGT
51+
MN908947.3 7672 7695 SARS-CoV-2_26_LEFT 2 + GCGAGAGACTTGTCACTACAGTT
52+
MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG
53+
MN908947.3 7997 8019 SARS-CoV-2_27_LEFT 1 + CTGATGTTGGTGATAGTGCGGA
54+
MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT 1 - AGCAATGTTGTGACTTTTTGCTACC
55+
MN908947.3 8304 8326 SARS-CoV-2_28_LEFT 2 + TGAAAACATGACACCCCGTGAC
56+
MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT 2 - TGACACCACCATCAATAGCCTTG
57+
MN908947.3 8596 8619 SARS-CoV-2_29_LEFT 1 + CTTGTGTTCCTTTTTGTTGCTGC
58+
MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT 1 - AGCCAAAACACAAGCTGATGTTG
59+
MN908947.3 8919 8944 SARS-CoV-2_30_LEFT 2 + ACCTAGAGTTTTTAGTGCAGTTGGT
60+
MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT 2 - CTACACCACAGAAAACTCCTGGT
61+
MN908947.3 9168 9192 SARS-CoV-2_31_LEFT 1 + CCTTGAAGGTTCTGTTAGAGTGGT
62+
MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC
63+
MN908947.3 9470 9497 SARS-CoV-2_32_LEFT 2 + GAGCTTTTGGTGAATACAGTCATGTAG
64+
MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT 2 - GAGGTAATAGCACATCACTACGCA
65+
MN908947.3 9782 9805 SARS-CoV-2_33_LEFT 1 + GTACTTTTGAAGAAGCTGCGCTG
66+
MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT 1 - TGTCTTGGACAGTAAACTACGTCATC
67+
MN908947.3 10076 10099 SARS-CoV-2_34_LEFT 2 + TCCCATCTGGTAAAGTTGAGGGT
68+
MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT 2 - CCACATGAACCATTAAGGAATGAACC
69+
MN908947.3 10393 10419 SARS-CoV-2_35_LEFT 1 + GTGTTAGCTTGTTACAATGGTTCACC
70+
MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT 1 - AGGTCCTAGTATGTCAACATGGTCT
71+
MN908947.3 10713 10742 SARS-CoV-2_36_LEFT 2 + CAATCGATTTACCACAACTCTTAATGACT
72+
MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT 2 - ACCCATAGCAAAAGGTAAAAAGGC
73+
MN908947.3 11000 11023 SARS-CoV-2_37_LEFT 1 + CACACCACTGGTTGTTACTCACA
74+
MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT 1 - GTGTCAAGACATTCATAAGTGTCCAC
75+
MN908947.3 11305 11330 SARS-CoV-2_38_LEFT 2 + GACTGTGTTATGTATGCATCAGCTG
76+
MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC
77+
MN908947.3 11624 11651 SARS-CoV-2_39_LEFT 1 + GCTATTTTTGTACTTGTTACTTTGGCC
78+
MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT 1 - CCCTGCATGGAAAGCAAAACAG
79+
MN908947.3 11937 11963 SARS-CoV-2_40_LEFT 2 + TGTCCAGTTACACAATGACATTCTCT
80+
MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT 2 - ACTTTTGCCCTCTTGTCCTCAG
81+
MN908947.3 12234 12255 SARS-CoV-2_41_LEFT 1 + ATTTGACCGTGATGCAGCCAT
82+
MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT 1 - AAGAGGCCATGCTAAATTAGGTGAA
83+
MN908947.3 12519 12546 SARS-CoV-2_42_LEFT 2 + TGGTACAACATTTACTTATGCATCAGC
84+
MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT 2 - TGTCTGTAACAAACCTACAAGGTGG
85+
MN908947.3 12831 12856 SARS-CoV-2_43_LEFT 1 + GGATTTGAAATGGGCTAGATTCCCT
86+
MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT 1 - CGATGCACCACCAAAGGATTCT
87+
MN908947.3 13124 13148 SARS-CoV-2_44_LEFT 2 + GGGGACAACCAATCACTAATTGTG
88+
MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT 2 - CATCAGTACTAGTGCCTGTGCC
89+
MN908947.3 13463 13485 SARS-CoV-2_45_LEFT 1 + TAAACGGGTTTGCGGTGTAAGT
90+
MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT 1 - TCACAATTACCTTCATCAAAATGCCT
91+
MN908947.3 13752 13775 SARS-CoV-2_46_LEFT 2 + AGAATAGACGGTGACATGGTACC
92+
MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT 2 - TCTACAACAGGAACTCCACTACCT
93+
MN908947.3 14045 14075 SARS-CoV-2_47_LEFT 1 + TGGTGTACTGACATTAGATAATCAAGATCT
94+
MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT 1 - TGGAACACCATCAACAAATATTTTTCTCA
95+
MN908947.3 14338 14362 SARS-CoV-2_48_LEFT 2 + ACTGTTTGGATGACAGATGCATTC
96+
MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT 2 - CAGAACTTCCTTCCTTAAAGAAACCC
97+
MN908947.3 14647 14674 SARS-CoV-2_49_LEFT 1 + ACAATGTTGCTTTTCAAACTGTCAAAC
98+
MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT 1 - GGGATGACATTACGTTTTGTATATGCG
99+
MN908947.3 14953 14983 SARS-CoV-2_50_LEFT 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT
100+
MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT 2 - GAGCAAGAACAAGTGAGGCCAT
101+
MN908947.3 15214 15237 SARS-CoV-2_51_LEFT 1 + GCAAATTCTATGGTGGTTGGCAC
102+
MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT 1 - GTCTGTGTTGTAAATTGCGGACA
103+
MN908947.3 15535 15557 SARS-CoV-2_52_LEFT 2 + CTGTCACGGCCAATGTTAATGC
104+
MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT 2 - GGATCTGGGTAAGGAAGGTACACA
105+
MN908947.3 15855 15881 SARS-CoV-2_53_LEFT 1 + ACTAAAGGACCTCATGAATTTTGCTC
106+
MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT 1 - GCAAAGAACACAAGCCCCAAC
107+
MN908947.3 16112 16137 SARS-CoV-2_54_LEFT 2 + ACATGATGAGTTAACAGGACACATG
108+
MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT 2 - CCAAAAACTTGTCCATTAGCACACA
109+
MN908947.3 16386 16408 SARS-CoV-2_55_LEFT 1 + AATGCTCCAGGTTGTGATGTCA
110+
MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT 1 - ACACGATAACCAGTAAAGACATAATTTCG
111+
MN908947.3 16692 16714 SARS-CoV-2_56_LEFT 2 + ACTGTACGTGAAGTGCTGTCTG
112+
MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT 2 - TGACTCTTACCAGTACCAGGTGG
113+
MN908947.3 16986 17013 SARS-CoV-2_57_LEFT 1 + GGCTTATACCCAACACTCAATATCTCA
114+
MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT 1 - CTGGCATTGACAACACTCAAATCA
115+
MN908947.3 17323 17345 SARS-CoV-2_58_LEFT 2 + TGCCTGAGACGACAGCAGATAT
116+
MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT 2 - TGTGGCCTGTTAATTGCAGATGA
117+
MN908947.3 17615 17642 SARS-CoV-2_59_LEFT 1 + GCTTAAAGCACATAAAGACAAATCAGC
118+
MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT 1 - TCCTACGTGGAATTTCAAGACTTGT
119+
MN908947.3 17911 17939 SARS-CoV-2_60_LEFT 2 + ACAGATTTAATGTTGCTATTACCAGAGC
120+
MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT 2 - TAGCATGACACCCCTCGACAT
121+
MN908947.3 18244 18267 SARS-CoV-2_61_LEFT 1 + ACCCTAACATGTTTATCACCCGC
122+
MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT 1 - GCTCAGGTCCTATTTTCACAAAATACTT
123+
MN908947.3 18550 18578 SARS-CoV-2_62_LEFT 2 + GTGACACACTTAAAAATCTCTCTGACAG
124+
MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT 2 - CCGCATTAATCTTCAGTTCATCACC
125+
MN908947.3 18869 18891 SARS-CoV-2_63_LEFT 1 + TAGGTGTCTAGCTGTCCACGAG
126+
MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT 1 - CCAGGCAAGTTAAGGTTAGATAGCA
127+
MN908947.3 19183 19208 SARS-CoV-2_64_LEFT 2 + GCCTATTTTGGAATTGCAATGTCGA
128+
MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT 2 - GTATCAAATTGTTTGTAAACCCACAAGC
129+
MN908947.3 19485 19513 SARS-CoV-2_65_LEFT 1 + GTCTGTAGACATCATGCTAATGAGTACA
130+
MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT 1 - GCTGGAGCATCTCTTTTGTAGTCC
131+
MN908947.3 19810 19836 SARS-CoV-2_66_LEFT 2 + AACCAGTACCAGAGGTGAAAATACTC
132+
MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT
133+
MN908947.3 20090 20117 SARS-CoV-2_67_LEFT 1 + CAAACAAGCTAGTCTTAATGGAGTCAC
134+
MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT 1 - AACACACACACTTAGATGAACCTGT
135+
MN908947.3 20377 20405 SARS-CoV-2_68_LEFT 2 + GACTAGCTAAACGTTTTAAGGAATCACC
136+
MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 - GCGACATTCATCATTATGCCTTTAGG
137+
MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 + CGGGTGTTGCTATGCCTAATCT
138+
MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC
139+
MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 + TTGATTGGTGATTGTGCAACTGTAC
140+
MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 - AGAATAGGAAGACAACTGAATTGGATTTG
141+
MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 + GGCAAACCACGCGAACAAATAG
142+
MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 - TGAGGATCTGAAAACTTTGTCAGGG
143+
MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAAC
144+
MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 - GTAGCGTTATTAACAATAAGTAGGGACTG
145+
MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 + AGAGGCTGGATTTTTGGTACTACT
146+
MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 - ACCTAGTGATGTTAATACCTATTGGCA
147+
MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 + TGGACCTTGAAGGAAAACAGGG
148+
MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA
149+
MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 + GAAAATGGAACCATTACAGATGCTGT
150+
MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 - TTTGCCCTGGAGCGATTTGT
151+
MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 + GCTGATTATTCTGTCCTATATAATTCCGC
152+
MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 - GTTGGAAACCATATGATTGTAAAGGAAAG
153+
MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA
154+
MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 - CACTGACACCACCAAAAGAACATG
155+
MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT
156+
MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 - GGATTGACTAGCTACACTACGTGC
157+
MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 + ACCCATTGGTGCAGGTATATGC
158+
MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT
159+
MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 + CCGTGCTTTAACTGGAATAGCTG
160+
MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 - GCAAATGGTATTTGTAATGCAGCAC
161+
MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 + TGCTCAATACACTTCTGCACTGT
162+
MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 - TGAAGTCTGCCTGTGATCAACC
163+
MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 + TGCACAAGCTTTAAACACGCTT
164+
MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 - CACGAGGAAAGTGTGCTTTTCC
165+
MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 + GCATGTGACTTATGTCCCTGCA
166+
MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 - AGATTCATTTAAATTCTTGGCAACCTCA
167+
MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 + GTTGATTTAGGTGACATCTCTGGCA
168+
MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 - AGCATCCTTGATTTCACCTTGCT
169+
MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 + ATGAAGACGACTCTGAGCCAGT
170+
MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT
171+
MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 + TGTTGTTTGTAACAGTTTACTCACACC
172+
MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 - TCAATTGAGTTGAGTACAGCTGGT
173+
MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 + GTGGTTATACTGAAAAATGGGAATCTGG
174+
MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 - AATCGAAGCGCAGTAAGGATGG
175+
MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 + CGTTTCGGAAGAGACAGGTACG
176+
MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 - ACAAAAACCTATTCCTGTTGGCATAG
177+
MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 + AAGCTCCTTGAACAATGGAACCT
178+
MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 - CAGCAATACGAAGATGTCCACGA
179+
MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 + ATTCTTCTCAACGTGCCACTCC
180+
MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 - TCCAAATGGAAACTTTAAAAGTCCTCA
181+
MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 + TCCAGTAGCAGTGACAATATTGCTT
182+
MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 - AGTGCAAATTTGTTATCAGCTAGAGG
183+
MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 + CACTACCAAGAGTGTGTTAGAGGTAC
184+
MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC
185+
MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 + TTGTTGCGGCAATAGTGTTTATAACA
186+
MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 - TGGGTGATTTAGAACCAGCCTC
187+
MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 + ACCCGTGTCCTATTCACTTCTATTC
188+
MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 - TTATTGGGTAAACCTTGGGGCC
189+
MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 + GTGCGTTGTTCGTTCTATGAAGAC
190+
MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 - ACCATCTTGGACTGAGATCTTTCATT
191+
MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 + AGATGACCAAATTGGCTACTACCG
192+
MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 - CCATTGCCAGCCATTCTAGCA
193+
MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 + TTCCTCATCACGTAGTCGCAAC
194+
MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 - CGACATTCCGAAGAACGCTGA
195+
MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 + CCAGGAACTAATCAGACAAGGAACT
196+
MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 - TTTAGGCCTGAGTTGAGTCAGC
197+
MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 + CTTCTTCCTGCTGCAGATTTGGA
198+
MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 - GCTATTAAAATCACATGGGGATAGCAC
199+
MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_alt1 2 + TGAATATCACTTTTGAACTTGATGAAAGGATTG
200+
MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_alt1 2 - GGTTGAAGAGCAGCAGAAGTG
201+
MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_alt1 1 - AGAATCTAAACCACTAAGACAAACACTAC
202+
MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_alt1 1 - AATGTTGTGACTTTTTGCTACCTGC
203+
MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_alt1 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT
204+
MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_alt1 2 - GTCCACAAACAGTTGCTGGTG
205+
MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_alt1 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC
206+
MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_alt1 2 + TTATGTACTCATTCGTTTCGGAAGAG
207+
MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_alt1 1 + TAGGTTTCCTATTCCTTACATGGATTTGT
208+
MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_alt1 1 - CTAGATGGTGTCCAGCAATACGAAG
209+
MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_alt1 2 - ATTAGTAATATCTCTGCTATAGTAACCTGAAAG

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