BWA-SW
Settings
Alignment Statistics
in %
Alignment Statistics
Sample | #Alignemnts | #Pairs | Properly Aligned in Pair | Aligned in Pair | Aligned (Singleton) | Unaligned | Not Primary Alignment | |
---|---|---|---|---|---|---|---|---|
Forward Reads | Reverse Reads | |||||||
Sample | #Alignemnts | Forward Reads | Reverse Reads | Properly Aligned in Pair | Aligned in Pair | Aligned (Singleton) | Unaligned | Not Primary Alignment |
#Pairs | ||||||||
{{ seqrun.sample }} | {{ seqrun["total alignments"] }} | {{ seqrun["read1"] }} | {{ seqrun["read2"] }} | {{ (seqrun["properly paired"] / seqrun["total alignments"] * 100).toFixed(2) }} | {{ ((seqrun["with itself and mate mapped"] - seqrun["properly paired"]) / seqrun["total alignments"] * 100).toFixed(2) }} | {{ (seqrun["singletons"] / seqrun["total alignments"] * 100).toFixed(2) }} | {{ (100 - (seqrun["singletons"] + seqrun["with itself and mate mapped"] + seqrun["secondary"] + seqrun["supplementary"] + seqrun["duplicates"]) / seqrun["total alignments"] * 100).toFixed(2) }} | {{ ((seqrun["secondary"] + seqrun["supplementary"] + seqrun["duplicates"]) / seqrun["total alignments"] * 100).toFixed(2) }} |
Sample | #Alignemnts | #Pairs | Properly Aligned in Pair | Aligned in Pair | Aligned (Singleton) | Unaligned | Not Primary Alignment | |
---|---|---|---|---|---|---|---|---|
Forward Reads | Reverse Reads | |||||||
Sample | #Alignemnts | Forward Reads | Reverse Reads | Properly Aligned in Pair | Aligned in Pair | Aligned (Singleton) | Unaligned | Not Primary Alignment |
#Pairs | ||||||||
{{ seqrun.sample }} | {{ seqrun["total alignments"] }} | {{ seqrun["read1"] }} | {{ seqrun["read2"] }} | {{ seqrun["properly paired"]}} | {{ seqrun["with itself and mate mapped"] - seqrun["properly paired"] }} | {{ seqrun["singletons"] }} | {{ seqrun["total alignments"] - seqrun["singletons"] - seqrun["with itself and mate mapped"] - seqrun["secondary"] - seqrun["supplementary"] - seqrun["duplicates"] }} | {{ seqrun["secondary"] + seqrun["supplementary"] + seqrun["duplicates"] }} |
Sample | #Reads | Aligned | Aligned [%] | Unaligned | Unaligned [%] |
---|---|---|---|---|---|
Sample | #Reads | Aligned | Aligned [%] | Unaligned | Unaligned [%] |
{{ seqrun.sample }} | {{ seqrun["total alignments"] / 2 }} | {{ seqrun["mapped"] }} | {{ (seqrun["mapped"] / seqrun["total alignments"] * 100).toFixed(2) }} | {{ seqrun["total alignments"] - seqrun["mapped"] }} | {{ ((1 - seqrun["mapped"] / seqrun["total alignments"]) * 100).toFixed(2) }} |