Input data and parameters 

Input

Analysis date: Tue Oct 31 17:40:58 GMT 2023
BAM file: SRX7354394.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): 35,968,400 / 35,877,814
Number of aligned pairs (without duplicates): 35,830,916
Total number of alignments: 77,017,935
Number of secondary alignments: 5,171,721
Number of non-unique alignments: 8,424,568
Aligned to genes: 61,166,382
Ambiguous alignments: 215,708
No feature assigned: 6,728,245
Missing chromosome in annotation: 483,032
Not aligned: 6,342,294

Reads genomic origin

Exonic: 61,166,382 / 90.09%
Intronic: 3,571,791 / 5.26%
Intergenic: 3,156,454 / 4.65%
Intronic/intergenic overlapping exon: 2,862,813 / 4.22%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.22
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 20,547,149
ACCT 5.52%
TCCT 4.63%
ATCT 4.32%
AGGT 4.29%
GCCT 3.54%
AGGA 2.89%
CCCT 2.63%
AGCT 2.38%
AGGC 2.24%
TTCT 2.23%
TCCC 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis