Input data and parameters 

Input

Analysis date: Sun Oct 29 01:18:06 GMT 2023
BAM file: SRX7354081.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): 38,997,959 / 38,958,479
Number of aligned pairs (without duplicates): 38,937,246
Total number of alignments: 87,057,297
Number of secondary alignments: 9,100,859
Number of non-unique alignments: 11,797,118
Aligned to genes: 66,015,687
Ambiguous alignments: 275,444
No feature assigned: 6,722,402
Missing chromosome in annotation: 2,246,646
Not aligned: 6,578,160

Reads genomic origin

Exonic: 66,015,687 / 90.76%
Intronic: 3,549,566 / 4.88%
Intergenic: 3,172,836 / 4.36%
Intronic/intergenic overlapping exon: 3,329,916 / 4.58%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.12
5'-3' bias: 2.41

Junction analysis

Reads at junctions: 20,382,730
ACCT 5.47%
TCCT 4.87%
AGGT 4.4%
ATCT 4.37%
CCCT 3.91%
AGGA 2.79%
AGGC 2.33%
AGAC 2.27%
GCCT 2.19%
AGCT 2.01%
GTCT 1.96%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis