Input data and parameters 

Input

Analysis date: Sun Oct 29 01:19:17 GMT 2023
BAM file: SRX7354108.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): 44,274,461 / 44,246,543
Number of aligned pairs (without duplicates): 44,240,878
Total number of alignments: 95,743,417
Number of secondary alignments: 7,222,413
Number of non-unique alignments: 10,808,642
Aligned to genes: 73,419,021
Ambiguous alignments: 314,130
No feature assigned: 10,102,820
Missing chromosome in annotation: 1,098,804
Not aligned: 2,139,304

Reads genomic origin

Exonic: 73,419,021 / 87.9%
Intronic: 7,539,952 / 9.03%
Intergenic: 2,562,868 / 3.07%
Intronic/intergenic overlapping exon: 3,333,188 / 3.99%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.23
5'-3' bias: 1.62

Junction analysis

Reads at junctions: 24,174,681
ACCT 5.26%
AGGT 4.66%
ATCT 3.8%
TCCT 3.69%
GCCT 3.4%
AGGA 3.36%
CCCT 2.68%
AGCT 2.65%
AGGC 2.42%
TTCT 2.11%
AGAT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis