Input data and parameters 

Input

Analysis date: Sun Oct 29 01:53:05 GMT 2023
BAM file: SRX7354055.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): 51,044,481 / 51,001,192
Number of aligned pairs (without duplicates): 50,986,108
Total number of alignments: 109,931,316
Number of secondary alignments: 7,885,643
Number of non-unique alignments: 12,852,376
Aligned to genes: 84,936,466
Ambiguous alignments: 330,641
No feature assigned: 11,116,317
Missing chromosome in annotation: 695,516
Not aligned: 2,076,971

Reads genomic origin

Exonic: 84,936,466 / 88.43%
Intronic: 7,779,510 / 8.1%
Intergenic: 3,336,807 / 3.47%
Intronic/intergenic overlapping exon: 3,956,451 / 4.12%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.25
5'-3' bias: 1.74

Junction analysis

Reads at junctions: 31,922,768
ACCT 5.49%
AGGT 4.59%
ATCT 3.69%
GCCT 3.62%
TCCT 3.56%
AGGA 3.2%
CCCT 2.69%
AGCT 2.66%
AGGC 2.38%
TTCT 2.26%
AGAT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis