Input data and parameters 

Input

Analysis date: Sun Oct 29 01:51:18 GMT 2023
BAM file: SRX7354162.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 43,287,942 / 43,257,926
Number of aligned pairs (without duplicates): 43,247,963
Total number of alignments: 95,645,390
Number of secondary alignments: 9,099,522
Number of non-unique alignments: 13,734,213
Aligned to genes: 72,355,230
Ambiguous alignments: 340,285
No feature assigned: 7,825,609
Missing chromosome in annotation: 1,390,053
Not aligned: 3,586,752

Reads genomic origin

Exonic: 72,355,230 / 90.24%
Intronic: 4,258,933 / 5.31%
Intergenic: 3,566,676 / 4.45%
Intronic/intergenic overlapping exon: 3,968,671 / 4.95%

Transcript coverage profile

5' bias: 0.07
3' bias: 0.1
5'-3' bias: 2.27

Junction analysis

Reads at junctions: 20,651,047
TCCT 5.65%
ACCT 5.1%
ATCT 4.55%
CCCT 4.54%
AGGT 4.19%
AGGA 2.74%
AGGC 2.27%
GCCT 2.15%
GTCT 2.13%
TTCT 2.07%
AGAC 1.89%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis