Input data and parameters 

Input

Analysis date: Tue Oct 31 09:08:55 GMT 2023
BAM file: SRX7354324.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): 35,684,245 / 35,643,785
Number of aligned pairs (without duplicates): 35,637,204
Total number of alignments: 76,468,431
Number of secondary alignments: 5,140,401
Number of non-unique alignments: 8,989,813
Aligned to genes: 60,862,463
Ambiguous alignments: 215,512
No feature assigned: 6,167,100
Missing chromosome in annotation: 233,543
Not aligned: 8,454,642

Reads genomic origin

Exonic: 60,862,463 / 90.8%
Intronic: 3,335,197 / 4.98%
Intergenic: 2,831,903 / 4.22%
Intronic/intergenic overlapping exon: 2,751,990 / 4.11%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.19
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 19,397,255
ACCT 5.77%
AGGT 4.76%
ATCT 3.76%
TCCT 3.7%
GCCT 3.36%
AGGA 3.29%
CCCT 2.54%
AGCT 2.42%
AGGC 2.39%
TTCT 2.24%
AGAT 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis