001、 在samtools flagstat 对bam的统计结果中,一共有三个比对率的结果: 002、比对率结果应该以哪个为准? 答案是:以3为准 003、以山羊、绵羊的fastq数据,绵羊的参考基因组进行比对测试 a、如果以primary mapped对比,基本看不出两者的差异(其中S是sheep,G是goat) b、 如果以 properly paired 比对率看,可以清晰...
samtools flagstat test.bam QC pass的reads的数量为68039736,未通过QC的reads数量为零,意味着总reads数为68039736 Mapped:比对到参考基因组上的reads数量 Paired:双端reads数据数量 Read1:R1的数量 Read2:R2的数量 Properly:完美匹配的reads数 PE中两条都比对到参考序列上的reads数单独一条匹配到参考序列上的reads数...
properly paired (95.96% : N/A) #完美匹配的reads数:比对到同一条参考序列,并且两条reads之间的距离符合设置的阈值 46308722 + 0 with itself and mate mapped #paired reads中两条都比对到参考序列上的reads数 596990 + 0 singletons (1.25% : N/A) #单独一条匹配到参考序列上的reads数,和上一个相加,...
samtools flagstat统计bam文件比对后每一个参数的解释如下: 14608455+0intotal(QC-passed reads+QC-failed reads)## reads总数37967+0secondary##出现比对到参考基因组多个位置的reads数0+0supplementary##可能存在嵌合的reads数0+0duplicates##重复的reads数14590894+0mapped(99.88%:N/A)##比对到参考基因组上的reads...
36727148 + 0 properly paired (94.51% : N/A) # 94.51%比例的reads成对的映射上 37160066 + 0 with itself and mate mapped # read映射上但配对read没映射上的数量 487819 + 0 singletons (1.26% : N/A) # 1.26%比例的read没映射上的同时,配对read映射上了 ...
samtools flagstat sample_name.sorted.bam > sample_name.flagstat.txt## 基本命令 a、生成的文件是一个包含16行的文本文件: 002、 (base) [b20223040323@admin2 workdir]$ cat Asiatic1.flagstat.txt## 查看统计结果622520785+0intotal (QC-passed reads + QC-failed reads)##不是总的reads, 为什么会出现奇...
samtools flagstat xx.bam 示例: 415088184 + 0 in total (QC-passed reads + QC-failed reads) 55152890 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 408418313 + 0 mapped (98.39% : N/A) 359935294 + 0 paired in sequencing 179967647 + 0 read1 ...
Usage: samtools flagstat <in.bam> $ samtools flagstat example.bam 11945742 + 0 in total (QC-passed reads + QC-failed reads) #总共的reads数 0 + 0 duplicates 7536364 + 0 mapped (63.09%:-nan%) #总体上reads的匹配率 11945742 + 0 paired in sequencing ...
properly paired both 0x1 and 0x2 bits set and 0x4 bit not set with itself and mate mapped 0x1 bit set and neither 0x4 nor 0x8 bits set singletons both 0x1 and 0x8 bits set and bit 0x4 not set And finally, two rows are given that additionally filter on the reference name (RNAM...
524 + 32 properly paired (99.05% : 88.89%) 524 + 32 with itself and mate mapped 5 + 4 singletons (0.95% : 11.11%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Mcnode1:~/cloud/adam/xubo/data/data_HDFS/adam$ samtool...