CARD注释结果文件说明
结果简介
微生物抗生素耐药性问题,是在人类为抑制病原微生物生长繁殖,而高频次、大剂量使用抗生素的背景下凸显出来的。微生物通过自身基因突变,或者在环境中由于基因水平转移,得到的这些（突变的）基因,使药物作用的靶位发生变异或药物不能正常地发挥作用,从而获得对特定抗生素的抗性。CARD(Comprehensive Antibiotic Resistance Database): 综合性抗生素抗性数据库,是目前使用最广泛的抗性基因数据库之一,目前包括约4000个抗性基因分类。
我们使用card_rgi分析工具,以CARD数据库作为参考数据库,对组装结果assembly.fasta文件,做细菌的抗生素抗性基因注释,找出基因组上的抗性基因,生成注释结果表格文件*.CARD.txt,推荐使用Excel或WPS软件来查看。
目录结构
CARD/ └── *.CARD.txt
格式说明
制表符分割的文本文档，使用 excel 打开。
文件内容举例如下：
文件内容说明如下：
| 列数 | 列标题 | 说明 |
|---|---|---|
| 1 | ORF_ID | Open Reading Frame identifier (internal to RGI) |
| 2 | Contig | Source Sequence |
| 3 | Start | Start co-ordinate of ORF |
| 4 | Stop | End co-ordinate of ORF |
| 5 | Orientation | Strand of ORF |
| 6 | Cut_Off | RGI Detection Paradigm (Perfect, Strict, Loose) |
| 7 | Pass_Bitscore | Strict detection model bitscore cut-off |
| 8 | Best_Hit_Bitscore | Bitscore value of match to top hit in CARD |
| 9 | Best_Hit_ARO | ARO term of top hit in CARD |
| 10 | Best_Identities | Percent identity of match to top hit in CARD |
| 11 | ARO | ARO accession of match to top hit in CARD |
| 12 | Model_type | CARD detection model type |
| 13 | SNPs_in_Best_Hit_ARO | Mutations observed in the ARO term of top hit in CARD (if applicable) |
| 14 | Other_SNPs | Mutations observed in ARO terms of other hits indicated by model id (if applicable) |
| 15 | Drug Class | ARO Categorization |
| 16 | Resistance Mechanism | ARO Categorization |
| 17 | AMR Gene Family | ARO Categorization |
| 18 | Predicted_DNA | ORF predicted nucleotide sequence |
| 19 | Predicted_Protein | ORF predicted protein sequence |
| 20 | CARD_Protein_Sequence | Protein sequence of top hit in CARD |
| 21 | Percentage Length of Reference Sequence | (length of ORF protein / length of CARD reference protein) |
| 22 | ID | HSP identifier (internal to RGI) |
| 23 | Model_id | CARD detection model id |
| 24 | Nudged | TRUE = Hit nudged from Loose to Strict |
| 25 | Note | Reason for nudge or other notes |
重要的信息包含在：第9~11列，第15~17列以及第21列。