Input data and parameters 

Input

Analysis date: Sun Oct 29 01:44:22 GMT 2023
BAM file: SRX7354106.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): 39,810,507 / 39,756,827
Number of aligned pairs (without duplicates): 39,748,364
Total number of alignments: 85,246,390
Number of secondary alignments: 5,679,056
Number of non-unique alignments: 9,062,760
Aligned to genes: 66,122,623
Ambiguous alignments: 291,438
No feature assigned: 9,241,341
Missing chromosome in annotation: 528,228
Not aligned: 2,190,528

Reads genomic origin

Exonic: 66,122,623 / 87.74%
Intronic: 6,780,137 / 9%
Intergenic: 2,461,204 / 3.27%
Intronic/intergenic overlapping exon: 4,248,179 / 5.64%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.23
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 26,659,668
ACCT 5.59%
AGGT 4.42%
TCCT 4.39%
ATCT 4.33%
GCCT 3.54%
CCCT 2.99%
AGGA 2.97%
AGGC 2.3%
AGCT 2.28%
TCCC 2.16%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis