Input data and parameters 

Input

Analysis date: Sun Oct 29 01:26:01 GMT 2023
BAM file: SRX7354093.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): 34,363,830 / 34,335,618
Number of aligned pairs (without duplicates): 34,332,658
Total number of alignments: 72,581,466
Number of secondary alignments: 3,882,018
Number of non-unique alignments: 6,591,576
Aligned to genes: 57,633,537
Ambiguous alignments: 165,409
No feature assigned: 7,930,936
Missing chromosome in annotation: 260,008
Not aligned: 5,652,016

Reads genomic origin

Exonic: 57,633,537 / 87.9%
Intronic: 4,864,754 / 7.42%
Intergenic: 3,066,182 / 4.68%
Intronic/intergenic overlapping exon: 2,335,073 / 3.56%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.17
5'-3' bias: 2.23

Junction analysis

Reads at junctions: 15,853,368
ACCT 5.34%
AGGT 4.93%
AGGA 3.68%
ATCT 3.65%
TCCT 3.43%
GCCT 2.9%
AGCT 2.72%
CCCT 2.38%
AGGC 2.36%
AGAT 2.31%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis