Skip to main content

Table 1 List of FASTQ reads dataset

From: Assessing Bos taurus introgression in the UOA Bos indicus assembly

Breeds N Read length Total reads Cov ARS_UCD1.2 (%) UOA_Brahman_1 (%)
Map Filt Ret Map Filt Ret
Angusa 9 151 172 7.26 97.65 13.74 83.91 97.77 14.99 82.77
Hereforda 8 99 242 10.17 99.34 15.83 83.51 99.47 17.26 82.21
Holsteina 9 100 124 4.58 93.37 16.82 76.55 93.45 17.91 75.54
Jerseya 7 100 186 6.86 98.79 19.79 79.00 98.84 20.84 78.00
Shorthorna 5 99 230 8.36 99.06 19.06 80.00 99.13 20.33 78.80
Simmentala 16 100 217 8.59 92.91 17.02 75.89 92.98 18.28 74.70
Bohaibc 3 150 222 12.21 99.55 25.12 74.44 99.68 26.40 73.28
Boranb 10 101 297 11.03 99.54 15.49 84.04 99.52 15.94 83.58
Brahmanb 7 114 283 11.64 88.74 3.98 84.76 89.84 4.58 85.26
Girb 9 99 91 3.27 97.09 12.40 84.69 95.64 12.32 83.33
Indian zebub 5 100 152 5.56 98.83 33.05 65.79 98.77 33.12 65.64
Kenanab 6 101 307 11.40 99.50 14.59 84.91 99.51 14.68 84.83
Mangshib 7 100 101 3.68 98.29 17.50 80.80 98.25 17.64 80.62
Neloreb 6 99 111 4.00 98.18 13.35 84.83 98.05 13.85 84.20
Ogadenb 5 101 291 10.80 99.51 15.65 83.86 99.49 16.11 83.38
  1. 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
  2. aBos taurus taurus
  3. bBos taurus indicus
  4. cHighly admixed with B. taurus ancestry