Assessing Bos taurus introgression in the UOA Bos indicus assembly

Table 1 List of FASTQ reads dataset

Breeds	N	Read length	Total reads	Cov	ARS_UCD1.2 (%)			UOA_Brahman_1 (%)
Breeds	N	Read length	Total reads	Cov	Map	Filt	Ret	Map	Filt	Ret
Angus^a	9	151	172	7.26	97.65	13.74	83.91	97.77	14.99	82.77
Hereford^a	8	99	242	10.17	99.34	15.83	83.51	99.47	17.26	82.21
Holstein^a	9	100	124	4.58	93.37	16.82	76.55	93.45	17.91	75.54
Jersey^a	7	100	186	6.86	98.79	19.79	79.00	98.84	20.84	78.00
Shorthorn^a	5	99	230	8.36	99.06	19.06	80.00	99.13	20.33	78.80
Simmental^a	16	100	217	8.59	92.91	17.02	75.89	92.98	18.28	74.70
Bohai^bc	3	150	222	12.21	99.55	25.12	74.44	99.68	26.40	73.28
Boran^b	10	101	297	11.03	99.54	15.49	84.04	99.52	15.94	83.58
Brahman^b	7	114	283	11.64	88.74	3.98	84.76	89.84	4.58	85.26
Gir^b	9	99	91	3.27	97.09	12.40	84.69	95.64	12.32	83.33
Indian zebu^b	5	100	152	5.56	98.83	33.05	65.79	98.77	33.12	65.64
Kenana^b	6	101	307	11.40	99.50	14.59	84.91	99.51	14.68	84.83
Mangshi^b	7	100	101	3.68	98.29	17.50	80.80	98.25	17.64	80.62
Nelore^b	6	99	111	4.00	98.18	13.35	84.83	98.05	13.85	84.20
Ogaden^b	5	101	291	10.80	99.51	15.65	83.86	99.49	16.11	83.38

N: Number of individuals; Read length: read length values were derived from the mode of read length from individuals raw reads from each respective breed; Total reads: total reads in million; Cov: coverage values were estimated from total bases in raw reads and using 2.7 Gb as the genome length; Map: mapped values were percentage of reads aligned to the respective reference genome; Filt: filter values were percentage of reads dropped from the BAM files due to not passing the parameters set during the base recalibration step in the genome analysis tool kit (GATK); Ret: retain values were percentage of reads passing the GATK base recalibration step and kept in the final BAM files for the next step of variants calling for the respective reference genome; All values for total reads, coverage values, mapped values, filter values, and retain values are averages of individuals for each respective breed
^aBos taurus taurus
^bBos taurus indicus
^cHighly admixed with B. taurus ancestry

ISSN: 1297-9686