Input data and parameters 

Input

Analysis date: Mon Oct 30 20:18:28 GMT 2023
BAM file: SRX7354248.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): 43,952,706 / 43,935,119
Number of aligned pairs (without duplicates): 43,910,265
Total number of alignments: 95,208,361
Number of secondary alignments: 7,320,536
Number of non-unique alignments: 11,875,802
Aligned to genes: 74,847,809
Ambiguous alignments: 278,911
No feature assigned: 7,544,234
Missing chromosome in annotation: 661,605
Not aligned: 3,592,109

Reads genomic origin

Exonic: 74,847,809 / 90.84%
Intronic: 4,301,060 / 5.22%
Intergenic: 3,243,174 / 3.94%
Intronic/intergenic overlapping exon: 3,308,996 / 4.02%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.15
5'-3' bias: 1.54

Junction analysis

Reads at junctions: 24,602,331
ACCT 4.85%
ATCT 4.82%
TCCT 4.6%
AGGT 4.41%
CCCT 3.5%
AGGA 2.84%
AGGC 2.5%
GCCT 2.26%
AGAC 2.14%
TTCT 2.03%
AGCT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis