Input data and parameters 

Input

Analysis date: Mon Oct 30 22:23:50 GMT 2023
BAM file: SRX7354259.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): 27,563,498 / 27,547,750
Number of aligned pairs (without duplicates): 27,545,396
Total number of alignments: 58,529,757
Number of secondary alignments: 3,418,509
Number of non-unique alignments: 5,649,810
Aligned to genes: 45,876,867
Ambiguous alignments: 161,165
No feature assigned: 6,587,530
Missing chromosome in annotation: 254,385
Not aligned: 2,233,346

Reads genomic origin

Exonic: 45,876,867 / 87.44%
Intronic: 4,195,522 / 8%
Intergenic: 2,392,008 / 4.56%
Intronic/intergenic overlapping exon: 1,867,215 / 3.56%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.21
5'-3' bias: 2.03

Junction analysis

Reads at junctions: 13,621,676
ACCT 5.44%
AGGT 4.83%
AGGA 3.58%
ATCT 3.54%
TCCT 3.53%
GCCT 3.03%
AGCT 2.75%
CCCT 2.57%
AGGC 2.44%
AGAT 2.3%
TTCT 2.08%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis