Controversies in modern evolutionary biology: the imperative for error detection and quality control

BMC Genomics

Table 3 Validation of putative protein sequence errors

	Putative protein errors^a	Genome errors^b		Exon conservation^c		Transcript evidence			% FP error^g
		Yes	No	Yes	No	No	Splicing variants^e	FP error prediction^f
Suspicious segment	223	161	62	43	19	12	3	4	1.8
Deletion	7	1	6	6	0	0	0	0	0.0
N-deletion	68	26	42	19	23	18	2	3	4.4
C-deletion	64	26	38	21	17	16	0	1	1.6
Deletion sub-total	362	214	148	89	59	46	5	8	2.9
	Putative protein errors	Genome errors		Intron conservation^d		Transcript evidence			% FP error
		Yes	No	Yes (stop)	No	No	Splicing variants	FP error prediction
Insertion	22	15	7	6 (1)	1	5	2	0	0.0
N-extension	18	7	11	7 (3)	4	7	1	3	16.7
C-extension	11	6	5	3 (1)	2	4	1	0	0.0
Insertion sub-total	51	28	23	16 (5)	7	16	4	3	5.9
Total	413	242	171	100	14	62	9	11	2.7

Putative errors were estimated by analyzing the corresponding gene sequences. ^aThe total number of protein sequence errors included in the analysis. ^bThe number of errors resulting from genome sequencing or assembly errors. ^cThe number of missing segments detected in the corresponding gene sequences. ^dThe number of errors resulting from alternative splicing variants reported for homologous genes. ^eThe number of inserted sequence segments detected in the gene sequences of homologous proteins. The number of these inserted sequence segments with at least one stop codon is given in brackets. ^fThe number of errors supported by transcript evidence, i.e. false positive (FP) error predictions. ^gThe percentage of the total number of putative errors that were invalidated by the analysis.

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