Table 5.

Gene prediction results in metagenomes of TS28 and TS50 from the twin study and SRX007415 from the rumen microbiota study

Metagenomes	Total reads	Average read length	Overlap of BLAST results (%)	FragGeneScan		MetaGene
				With indel model	Without indel modela
TS28	312 665	329	50	94.54	82.26	76.10
			100	92.08	54.98	46.47
TS50	622 554	200	50	93.31	88.38	81.20
			100	92.25	81.35	68.69
SRX007415	1 164 805	72	50	85.84	68.14	–b
			100	85.80	68.10	–

^aThis experiment was carried out to demonstrate how much improvement gene prediction gained by considering indels.

^bMetaGene only works with reads that are of at least 100 bases.