Input data and parameters 

Input

Analysis date: Tue Oct 31 18:08:09 GMT 2023
BAM file: SRX7354403.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): 53,575,022 / 53,530,134
Number of aligned pairs (without duplicates): 53,521,751
Total number of alignments: 113,705,171
Number of secondary alignments: 6,600,015
Number of non-unique alignments: 11,095,750
Aligned to genes: 88,668,174
Ambiguous alignments: 284,189
No feature assigned: 13,266,174
Missing chromosome in annotation: 390,884
Not aligned: 9,399,940

Reads genomic origin

Exonic: 88,668,174 / 86.99%
Intronic: 8,399,372 / 8.24%
Intergenic: 4,866,802 / 4.77%
Intronic/intergenic overlapping exon: 3,678,841 / 3.61%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.19
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 28,778,570
ACCT 5.38%
AGGT 4.64%
ATCT 3.75%
TCCT 3.6%
AGGA 3.47%
GCCT 3.25%
AGCT 2.66%
AGGC 2.46%
CCCT 2.41%
AGAT 2.25%
TTCT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis