Input data and parameters 

Input

Analysis date: Tue Oct 31 09:39:09 GMT 2023
BAM file: SRX7354313.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): 46,129,012 / 46,097,352
Number of aligned pairs (without duplicates): 46,081,646
Total number of alignments: 102,923,380
Number of secondary alignments: 10,697,016
Number of non-unique alignments: 15,448,282
Aligned to genes: 76,809,627
Ambiguous alignments: 323,984
No feature assigned: 8,582,873
Missing chromosome in annotation: 1,758,614
Not aligned: 6,293,870

Reads genomic origin

Exonic: 76,809,627 / 89.95%
Intronic: 4,911,703 / 5.75%
Intergenic: 3,671,170 / 4.3%
Intronic/intergenic overlapping exon: 3,282,615 / 3.84%

Transcript coverage profile

5' bias: 0.05
3' bias: 0.09
5'-3' bias: 2.51

Junction analysis

Reads at junctions: 19,910,452
TCCT 6.7%
CCCT 6.21%
ACCT 4.84%
ATCT 4.83%
AGGT 3.58%
AGGA 2.81%
GTCT 2.51%
TCCG 2.11%
TTCT 1.96%
AGGC 1.93%
GCCT 1.88%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis