Input data and parameters 

Input

Analysis date: Mon Oct 30 12:51:26 GMT 2023
BAM file: SRX7354189.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): 46,432,967 / 46,419,069
Number of aligned pairs (without duplicates): 46,411,582
Total number of alignments: 98,680,789
Number of secondary alignments: 5,828,753
Number of non-unique alignments: 9,364,018
Aligned to genes: 79,643,448
Ambiguous alignments: 287,049
No feature assigned: 8,805,015
Missing chromosome in annotation: 581,259
Not aligned: 2,357,498

Reads genomic origin

Exonic: 79,643,448 / 90.05%
Intronic: 5,659,393 / 6.4%
Intergenic: 3,145,622 / 3.56%
Intronic/intergenic overlapping exon: 3,140,764 / 3.55%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.15
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 24,433,218
ACCT 5.37%
AGGT 4.86%
ATCT 3.79%
TCCT 3.71%
AGGA 3.6%
GCCT 3.06%
AGCT 2.61%
CCCT 2.45%
AGGC 2.3%
AGAT 2.09%
TTCT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis