Input data and parameters 

Input

Analysis date: Mon Oct 30 22:35:24 GMT 2023
BAM file: SRX7354237.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): 47,669,839 / 47,627,367
Number of aligned pairs (without duplicates): 47,612,868
Total number of alignments: 102,191,557
Number of secondary alignments: 6,894,351
Number of non-unique alignments: 10,774,188
Aligned to genes: 80,864,859
Ambiguous alignments: 262,963
No feature assigned: 9,612,743
Missing chromosome in annotation: 676,804
Not aligned: 5,377,254

Reads genomic origin

Exonic: 80,864,859 / 89.38%
Intronic: 6,952,575 / 7.68%
Intergenic: 2,660,168 / 2.94%
Intronic/intergenic overlapping exon: 3,898,836 / 4.31%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.22
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 28,975,106
AGGT 4.86%
ACCT 4.84%
ATCT 4.76%
TCCT 4.28%
AGGA 3.45%
AGCT 2.82%
GCCT 2.64%
AGGC 2.35%
CCCT 2.29%
AGAT 1.94%
TTCT 1.83%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis