Input data and parameters 

Input

Analysis date: Tue Oct 31 01:43:06 GMT 2023
BAM file: SRX7354300.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): 35,014,892 / 34,979,736
Number of aligned pairs (without duplicates): 34,975,247
Total number of alignments: 74,856,037
Number of secondary alignments: 4,861,409
Number of non-unique alignments: 7,640,721
Aligned to genes: 56,256,465
Ambiguous alignments: 236,793
No feature assigned: 10,122,166
Missing chromosome in annotation: 599,892
Not aligned: 9,356,718

Reads genomic origin

Exonic: 56,256,465 / 84.75%
Intronic: 6,067,673 / 9.14%
Intergenic: 4,054,493 / 6.11%
Intronic/intergenic overlapping exon: 2,305,369 / 3.47%

Transcript coverage profile

5' bias: 0.59
3' bias: 0.28
5'-3' bias: 1.69

Junction analysis

Reads at junctions: 22,725,376
ACCT 5.26%
AGGT 4.8%
AGGA 3.51%
TCCT 3.45%
ATCT 3.35%
GCCT 3.33%
AGCT 2.81%
CCCT 2.74%
AGGC 2.48%
AGAT 2.23%
TTCT 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