Input data and parameters 

Input

Analysis date: Tue Oct 31 00:18:40 GMT 2023
BAM file: SRX7354291.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): 29,969,050 / 29,956,669
Number of aligned pairs (without duplicates): 29,952,683
Total number of alignments: 67,712,871
Number of secondary alignments: 7,787,152
Number of non-unique alignments: 10,685,637
Aligned to genes: 42,211,088
Ambiguous alignments: 186,362
No feature assigned: 12,967,889
Missing chromosome in annotation: 1,661,895
Not aligned: 727,703

Reads genomic origin

Exonic: 42,211,088 / 76.5%
Intronic: 5,976,040 / 10.83%
Intergenic: 6,991,849 / 12.67%
Intronic/intergenic overlapping exon: 2,172,805 / 3.94%

Transcript coverage profile

5' bias: 0.2
3' bias: 0.18
5'-3' bias: 2.12

Junction analysis

Reads at junctions: 17,572,994
TCCT 5.42%
ACCT 5.26%
ATCT 4.47%
AGGT 3.97%
CCCT 3.22%
GCCT 2.96%
AGGA 2.63%
TCCC 2.56%
GTCT 2.48%
TTCT 2.42%
AGGC 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis