Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

Table 1 Count of transcripts where the 5′ most ORF is a recognised ORF

Feature	Count	Percent of total	Average poly A length of the dominant transcript
Total of all features	72,172
N	27,882	38.6327	55
None from list	10,453	14.4834	58
M	10,367	14.3642	55
ORF 7a	5162	7.1523	60
ORF 7b	4786	6.6313	61
ORF 3a	3449	4.7788	56
ORF 6	2649	3.6703	56
ORF 8	1447	2.0049	57
E	930	1.2885	56
ORF 9a	530	0.7343	56
S glycoprotein Bristol deletion	86	0.1191	55
S glycoprotein	33	0.0457	54
ORF 3b	6	0.0083	43
ORF 9b	6	0.0083	56
ORF 10	2	0.0027	51

Only transcripts that start to map within the expected leader TRS are considered. For each transcript group, the average polyA length is also shown for the dominant transcript that codes for the indicated ORF. Note that around 14% of transcripts do not apparently code for a known ORF, noted as “none from list”

ISSN: 1756-994X