TABLE 1.

Details of the 27 P. pastoris strains analyzed by next-generation sequencing^f

No.	Identifier	Vector	Linearization	Integration	Group	Replicate	SNPs and indelsc	Estimated CNd			Integration locus
								SAMtools	TPM	Rounded
1	wt/mutSa	Control	NA	NA	NA	NA	37e (15 in exons)	NA	NA	NA	NA
2	QTV19b	Control	NA	NA	NA	NA	27e (11 in exons)	NA	NA	NA	NA
3	QTV76	GUT1 vector	SwaI	Specific	Avg	1	1 (intergenic)	0.6058	0.6768	1	GUT1
4	QTV77	GUT1 vector	SwaI	Specific	Avg	2	2 (intergenic)	0.6608	0.5824	1	GUT1
5	QTV78	GUT1 vector	SwaI	Specific	Avg	3	5 (intergenic, one mitochondrial intergenic)	0.7201	0.6951	1	GUT1
6	QTV79	GUT1 vector	SwaI	Nonspecific	Avg	1	3 (2 in exons, 1 intergenic)	0.7010	0.5707	1	Chromosome 2: 3,438,50 bp in ACIB2EUKG769578
7	QTV80	GUT1 vector	SwaI	Nonspecific	Avg	2	3 (1 in exon, 2 intergenic)	0.8522	0.7346	1	Chromosome 2: 1,536,800 bp between two genes
8	QTV81	GUT1 vector	SwaI	Nonspecific	Avg	3	2 (intergenic)	0.9243	0.8395	1	Chromosome 2: 1,472,800 bp, no annotation
9	QTV82	GUT1 vector	SwaI	Nonspecific	High	1	2 (1 in exon, 1 intergenic)	1.8054	1.7745	2	Chromosome 4: 6,794,00 bp near ACIB2EUKG772429
10	QTV83	GUT1 vector	SwaI	Nonspecific	High	2	2 (1 intergenic, 1 mitochondrial intergenic)	1.4162	1.3572	1	Chromosome 1: 1,994,650 bp, ACIB2EUKG768896
11	QTV84	GUT1 vector	SwaI	Nonspecific	Low/no	1	23 (intergenic)	1.2110	1.1716	1	∼69-kbp deletion at the end of chromosome 4: 1,752,000–1,821,000 bp; 17 genes deleted
12	QTV85	GUT1 vector	SwaI		Low/no	2	1 (exon)	0.7803	0.6157	1	Chromosome 1: 1,579,000 bp, ∼550 bp deleted between ACIB2EUKG768656 and ACIB2EUKG768657
13	QTV86	GUT1 vector	SacI		Avg (lower)	1	2 (1 intergenic, 1 mitochondrial intergenic)	1.0203	0.7384	1	Chromosome 4: 2,380,00 bp in AOX1 promoter
14	QTV87	GUT1 vector	SacI		Avg (lower)	2	2 (intergenic)	0.8369	0.7783	1	Not found
15	QTV88	GUT1 vector	SacI		Avg (lower)	3	3 (1 in exon, 2 intergenic)	0.8240	0.7028	1	Not found
16	QTV89	GUT1 vector	SacI		Avg (higher)	1	3 (intergenic)	0.8657	0.7019	1	Not found
17	QTV90	GUT1 vector	SacI		Avg (higher)	2	10 (1 intergenic, others in same gene)	0.8637	0.7428	1	Not found
18	QTV91	GUT1 vector	SacI		Avg (higher)	3	1 (intergenic)	0.8371	0.7704	1	Not found
19	QTV92	GUT1 vector	SacI		High	1	6 (1 in exon, 5 intergenic)	1.8785	2.0084	2	Not found
20	QTV93	GUT1 vector	SacI		High	2	4 (3 intergenic, 1 mitochondrial intergenic)	2.0182	2.1124	2	Not found
21	QTV94	GUT1 vector	SacI		High	3	2 (1 in an exon, 1 intergenic)	2.2047	2.3392	2	Not found
22	QTV95	STD T4	SacI		High	1	1 (intergenic)	2.3142	2.3378	2	Not found
23	QTV96	STD T4	SacI		High	2	1 (intergenic)	4.6788	4.7903	5	Not found
24	QTV97	STD T4	SacI		High	3	2 (intergenic)	4.9057	4.9626	5	Not found
25	QTV98	STD T4	SacI		Avg	1	1 (intergenic)	0.8635	0.8346	1	Not found
26	QTV99	STD T4	SacI		Avg	2	1 (intergenic)	0.8234	0.7851	1	Not found
27	QTV100	STD T4	SacI		Avg	3	10 (2 in mitochondrial genes, rest intergenic)	1.3011	1.3548	1	Not found

^aUnmodified parental strain (mut^S).

^bEmpty transformation (without DNA) of the unmodified parental/reference strain wt/mut^S (to check if electroporation procedure for transformation of DNA has a negative effect).

^cNumber of unique variants with a quality score of >20 using bcfvariant tools (i.e., unique compared to the mut^S reference strain).

^dSee Table S7 in the supplemental material for details on the copy number calculation methods SAMtools (BAM stats) and TPM.

^eRelative to the PacBio reference sequence (23).

^fNA, not applicable.