Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Whole-Genome Data
2.2. Read Mapping and SNP Calling
2.3. Identification of InDels
2.4. Variant Functional Annotation and GO Enrichment
3. Results
3.1. Read Alignment
3.2. Identification of SNPs and InDels
3.3. Functional Annotation of SNPs and InDels
3.4. GO Analysis of the SNPs and InDels
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Breed | Sample ID | SRR ID | Total Reads | Aligned Reads Rate (%) | Duplication Rate (%) | Average Read Depth |
---|---|---|---|---|---|---|
WS | WS1 | SRR6024561 | 132599505 | 131966081 (99.52%) | 5.24% | 6.7367× |
WS2 | SRR6024562 | 210348316 | 208908938 (99.32%) | 7.57% | 10.9981× | |
WS3 | SRR6024569 | 213171893 | 209992479 (98.51%) | 7.56% | 11.0636× | |
WS4 | SRR6024575 | 220677796 | 219684659 (99.55%) | 7.58% | 10.6536× | |
WS5 | SRR6024576 | 185678168 | 184843226 (99.55%) | 6.60% | 9.3981× | |
WS6 | SRR6024577 | 220875686 | 219906218 (99.56%) | 7.17% | 11.5984× | |
WS7 | SRR6024578 | 124034762 | 123493668 (99.56%) | 5.40% | 6.5332× | |
WN | WN4 | SRR5507199 | 453240314 | 443641290 (97.88%) | 10.12% | 22.9631× |
WN8 | SRR5507198 | 453327732 | 448362891 (98.9%) | 9.91% | 23.1603× | |
WN9 | SRR5507195 | 189321051 | 187411280 (98.99%) | 5.63% | 9.6483× | |
WN10 | SRR5507196 | 203146450 | 201321637 (99.1%) | 6.00% | 10.1569× | |
WN11 | SRR5507197 | 229615463 | 228096174 (99.34%) | 6.33% | 11.7816× | |
LQ | LQ5 | SRR5507190 | 229615463 | 228096174 (99.34%) | 6.33% | 11.5007× |
LQ12 | SRR5507189 | 219526027 | 217652138 (99.15%) | 6.14% | 11.1222× | |
LQ15 | SRR5507188 | 208719494 | 207367555 (99.35%) | 5.91% | 10.6481× |
Fields | LQ | WN | WS |
---|---|---|---|
Total number | 19,178,051 | 23,091,150 | 23,431,130 |
3 prime UTR | 390,813 | 481,642 | 500,217 |
5 prime UTR | 110,542 | 137,007 | 146,969 |
Downstream gene | 4,673,996 | 5,721,422 | 5,884,594 |
Initiator codon | 25 | 31 | 39 |
Intergenic region | 10,333,593 | 12,409,887 | 12,561,984 |
Intragenic | 13,622,957 | 16,715,251 | 17,111,225 |
Intron | 85,061,834 | 100,821,955 | 105,226,537 |
Missense | 138,168 | 173,641 | 212,294 |
Non coding transcript exon | 172,858 | 212,090 | 223,022 |
Non coding transcript | 32,436,546 | 39,244,542 | 39,287,003 |
Splice acceptor | 717 | 900 | 887 |
Splice donor | 857 | 1152 | 1129 |
Splice region | 59,437 | 74,604 | 79,809 |
Start lost | 246 | 273 | 329 |
Stop gained | 1108 | 1253 | 1476 |
Stop lost | 211 | 273 | 263 |
Stop retained | 221 | 246 | 258 |
Synonymous | 278,880 | 348,230 | 528,134 |
Upstream gene | 4,538,595 | 5,552,247 | 5,651,124 |
Novel | 4,354,976 | 5,288,934 | 5,226,594 |
Known | 14,823,074 | 17,802,215 | 18,204,535 |
Fields | LQ | WN | WS |
---|---|---|---|
Total number | 2,153,542 | 2,586,758 | 2,471,063 |
3 prime UTR | 54,892 | 67,465 | 65,837 |
5 prime UTR | 9904 | 12,229 | 12,421 |
Bidirectional gene fusion | 80 | 83 | 139 |
Conservative inframe deletion | 561 | 814 | 1021 |
Conservative inframe insertion | 434 | 546 | 781 |
Disruptive inframe deletion | 1039 | 1292 | 1735 |
Disruptive inframe insertion | 483 | 583 | 955 |
Downstream gene | 585,215 | 719,779 | 693,994 |
Frameshift variant | 4168 | 5516 | 9559 |
Gene fusion | 198 | 178 | 232 |
Intergenic region | 1152,941 | 1,382,145 | 1,318,068 |
Intragenic | 1,485,117 | 1,817,239 | 1,775,709 |
Intron | 9,407,833 | 11,108,642 | 10,992,364 |
Non coding transcript exon | 17,425 | 21,355 | 21,201 |
Non coding transcript | 3,688,414 | 4,441,858 | 4,170,309 |
Splice acceptor | 384 | 451 | 471 |
Splice donor | 368 | 412 | 477 |
Splice region | 6396 | 7787 | 8542 |
Start lost | 58 | 64 | 54 |
Stop gained | 57 | 73 | 131 |
Stop lost | 32 | 73 | 61 |
Upstream gene | 54,6024 | 666,968 | 642,273 |
GO Biological Process Complete | Count | Fold Enrichment | FDR |
---|---|---|---|
Smell | |||
Sensory perception of smell (GO:0007608) | 104 | 3.05 | 2.78 × 10−18 |
Detection of chemical stimulus involved in sensory perception of smell (GO:0050911) | 101 | 3.03 | 5.15 × 10−18 |
Sensory perception of chemical stimulus (GO:0007606) | 104 | 2.96 | 4.27 × 10−18 |
Detection of chemical stimulus involved in sensory perception (GO:0050907) | 101 | 2.99 | 6.22 × 10−18 |
Immune responses | |||
Complement activation (GO:0006956) | 9 | 7.5 | 3.92 × 10−3 |
Humoral immune response (GO:0006959) | 11 | 4.72 | 1.62 × 10−2 |
Complement activation, classical pathway (GO:0006958) | 6 | 9.21 | 3.29 × 10−2 |
Activation of immune response (GO:0002253) | 16 | 3.01 | 4.58 × 10−2 |
Metabolic process | |||
Metabolic process (GO:0008152) | 114 | 0.57 | 2.55 × 10−10 |
Organic substance metabolic process (GO:0071704) | 98 | 0.56 | 2.16 × 10−9 |
Cellular metabolic process (GO:0044237) | 87 | 0.54 | 2.92 × 10−9 |
Primary metabolic process (GO:0044238) | 95 | 0.57 | 5.67 × 10−8 |
Organonitrogen compound metabolic process (GO:1901564) | 64 | 0.55 | 4.18 × 10−5 |
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Zhang, F.; Qu, K.; Chen, N.; Hanif, Q.; Jia, Y.; Huang, Y.; Dang, R.; Zhang, J.; Lan, X.; Chen, H.; et al. Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds. Animals 2019, 9, 596. https://doi.org/10.3390/ani9090596
Zhang F, Qu K, Chen N, Hanif Q, Jia Y, Huang Y, Dang R, Zhang J, Lan X, Chen H, et al. Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds. Animals. 2019; 9(9):596. https://doi.org/10.3390/ani9090596
Chicago/Turabian StyleZhang, Fengwei, Kaixing Qu, Ningbo Chen, Quratulain Hanif, Yutang Jia, Yongzhen Huang, Ruihua Dang, Jicai Zhang, Xianyong Lan, Hong Chen, and et al. 2019. "Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds" Animals 9, no. 9: 596. https://doi.org/10.3390/ani9090596