Analysis of ACTIV trace data for checking concordance between illumina and ONT¶

(412, 10)

Number of SRRs = 412

Number of biosample = 154

Number of bioprojects = 9

Library selection methods = ["PCR", "Random", "RT-PCR"]

Number of sequencing centers = 12

Total number of samples run with EC-19 = 406¶

	acc	mapped_reads	ref_recovery_perc	avg_fold	std_fold	biosample	platform	librarylayout	primer_info
0	ERR4364963	1449899	99.7924	6731.29	8491.87	SAMEA7080096	ILLUMINA	PAIRED	ARTIC-V3
1	ERR4365125	1730349	92.6984	7975.84	14620.46	SAMEA7080256	ILLUMINA	PAIRED	ARTIC-V3
2	ERR4365209	3248384	99.8159	15139.40	15217.73	SAMEA7080342	ILLUMINA	PAIRED	ARTIC-V3
3	ERR4421397	628713	99.9431	2966.24	1732.06	SAMEA7080329	ILLUMINA	PAIRED	ARTIC-V3
4	ERR4421538	493422	99.9263	2297.76	1330.58	SAMEA7080380	ILLUMINA	PAIRED	ARTIC-V3
...	...	...	...	...	...	...	...	...	...
402	SRR13870634	184947	100.0000	4189.80	2088.22	SAMN18188239	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
403	SRR13870635	224223	100.0000	4502.01	2545.61	SAMN18188238	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
404	SRR13870636	217183	100.0000	4960.81	2519.76	SAMN18188237	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
405	SRR13870638	277994	100.0000	6099.10	3349.11	SAMN18188234	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
406	SRR13870639	294766	100.0000	6940.63	3649.40	SAMN18188233	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq

407 rows × 9 columns

	acc	mapped_reads	ref_recovery_perc	avg_fold	std_fold	biosample	platform	librarylayout	primer_info
0	ERR4364963	1449899	99.7924	6731.29	8491.87	SAMEA7080096	ILLUMINA	PAIRED	ARTIC-V3
1	ERR4365125	1730349	92.6984	7975.84	14620.46	SAMEA7080256	ILLUMINA	PAIRED	ARTIC-V3
2	ERR4365209	3248384	99.8159	15139.40	15217.73	SAMEA7080342	ILLUMINA	PAIRED	ARTIC-V3
3	ERR4421397	628713	99.9431	2966.24	1732.06	SAMEA7080329	ILLUMINA	PAIRED	ARTIC-V3
4	ERR4421538	493422	99.9263	2297.76	1330.58	SAMEA7080380	ILLUMINA	PAIRED	ARTIC-V3
...	...	...	...	...	...	...	...	...	...
402	SRR13870634	184947	100.0000	4189.80	2088.22	SAMN18188239	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
403	SRR13870635	224223	100.0000	4502.01	2545.61	SAMN18188238	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
404	SRR13870636	217183	100.0000	4960.81	2519.76	SAMN18188237	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
405	SRR13870638	277994	100.0000	6099.10	3349.11	SAMN18188234	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq
406	SRR13870639	294766	100.0000	6940.63	3649.40	SAMN18188233	OXFORD_NANOPORE	SINGLE	Tiled-ClickSeq

307 rows × 9 columns

	Group_Name	Accession	Pos	Ref	Alt	DP	G_AD_2	Alt_Freq	biosample	platform	bioproject	center_name	librarylayout	libraryselection	librarysource	attributes	ec-19_run_with_primer_trim
0	LANL	ERR4364963	241	C	T	3510	3441	0.9806	SAMEA7080096	ILLUMINA	PRJEB37886	ORIGINATING LAB: WALES SPECIALIST VIROLOGY CEN...	PAIRED	PCR	VIRAL RNA	ena_last_update_sam: 2020-07-22;sample_capture...	artic_primer_v3
1	LANL	ERR4364963	3037	C	T	1752	1750	0.9994	SAMEA7080096	ILLUMINA	PRJEB37886	ORIGINATING LAB: WALES SPECIALIST VIROLOGY CEN...	PAIRED	PCR	VIRAL RNA	ena_last_update_sam: 2020-07-22;sample_capture...	artic_primer_v3
2	LANL	ERR4364963	4186	T	C	6464	6462	0.9998	SAMEA7080096	ILLUMINA	PRJEB37886	ORIGINATING LAB: WALES SPECIALIST VIROLOGY CEN...	PAIRED	PCR	VIRAL RNA	ena_last_update_sam: 2020-07-22;sample_capture...	artic_primer_v3
3	LANL	ERR4364963	11801	G	A	6513	6511	0.9997	SAMEA7080096	ILLUMINA	PRJEB37886	ORIGINATING LAB: WALES SPECIALIST VIROLOGY CEN...	PAIRED	PCR	VIRAL RNA	ena_last_update_sam: 2020-07-22;sample_capture...	artic_primer_v3
4	LANL	ERR4364963	14408	C	T	6418	6414	0.9995	SAMEA7080096	ILLUMINA	PRJEB37886	ORIGINATING LAB: WALES SPECIALIST VIROLOGY CEN...	PAIRED	PCR	VIRAL RNA	ena_last_update_sam: 2020-07-22;sample_capture...	artic_primer_v3

	Accession	Pos	Ref	Alt	DP	G_AD_2	Alt_Freq	biosample	platform	bioproject	librarylayout	libraryselection	librarysource	ec-19_run_with_primer_trim	mapped_reads	avg_fold	std_fold	ref_recovery_perc	primer_info	primer_info2
0	ERR4364963	241	C	T	3510	3441	0.9806	SAMEA7080096	ILLUMINA	PRJEB37886	PAIRED	PCR	VIRAL RNA	artic_primer_v3	1449899	6731.29	8491.87	99.7924	ARTIC-V3	ARTIC-V3
1	ERR4364963	3037	C	T	1752	1750	0.9994	SAMEA7080096	ILLUMINA	PRJEB37886	PAIRED	PCR	VIRAL RNA	artic_primer_v3	1449899	6731.29	8491.87	99.7924	ARTIC-V3	ARTIC-V3
2	ERR4364963	4186	T	C	6464	6462	0.9998	SAMEA7080096	ILLUMINA	PRJEB37886	PAIRED	PCR	VIRAL RNA	artic_primer_v3	1449899	6731.29	8491.87	99.7924	ARTIC-V3	ARTIC-V3
3	ERR4364963	11801	G	A	6513	6511	0.9997	SAMEA7080096	ILLUMINA	PRJEB37886	PAIRED	PCR	VIRAL RNA	artic_primer_v3	1449899	6731.29	8491.87	99.7924	ARTIC-V3	ARTIC-V3
4	ERR4364963	14408	C	T	6418	6414	0.9995	SAMEA7080096	ILLUMINA	PRJEB37886	PAIRED	PCR	VIRAL RNA	artic_primer_v3	1449899	6731.29	8491.87	99.7924	ARTIC-V3	ARTIC-V3
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
7045	SRR13870670	11673	A	A(R)	5821	2064	0.3546	SAMN18188238	ILLUMINA	PRJNA707211	PAIRED	RT-PCR	VIRAL RNA	NaN	6513244	30875.05	29860.30	99.9933	RNA-Seq	no-primer
7046	SRR13870670	14220	C	T(Y)	7378	5034	0.6823	SAMN18188238	ILLUMINA	PRJNA707211	PAIRED	RT-PCR	VIRAL RNA	NaN	6513244	30875.05	29860.30	99.9933	RNA-Seq	no-primer
7047	SRR13870670	14408	C	T	7909	7871	0.9952	SAMN18188238	ILLUMINA	PRJNA707211	PAIRED	RT-PCR	VIRAL RNA	NaN	6513244	30875.05	29860.30	99.9933	RNA-Seq	no-primer
7048	SRR13870670	23403	A	G	7697	7593	0.9866	SAMN18188238	ILLUMINA	PRJNA707211	PAIRED	RT-PCR	VIRAL RNA	NaN	6513244	30875.05	29860.30	99.9933	RNA-Seq	no-primer
7049	SRR13870670	25563	G	T	7826	7787	0.9951	SAMN18188238	ILLUMINA	PRJNA707211	PAIRED	RT-PCR	VIRAL RNA	NaN	6513244	30875.05	29860.30	99.9933	RNA-Seq	no-primer

4252 rows × 20 columns

'SAMEA7080096'

<function __main__.create_venn(df, bio_samp)>

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Analysis of ACTIV trace data for checking concordance between illumina and ONT¶

Total number of samples run with EC-19 = 406¶