Input data and parameters 

Input

Analysis date: Mon Oct 30 20:27:48 GMT 2023
BAM file: SRX7354202.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): 39,847,832 / 39,815,823
Number of aligned pairs (without duplicates): 39,810,983
Total number of alignments: 84,653,268
Number of secondary alignments: 4,989,613
Number of non-unique alignments: 8,406,337
Aligned to genes: 69,070,285
Ambiguous alignments: 248,188
No feature assigned: 6,615,683
Missing chromosome in annotation: 312,775
Not aligned: 5,957,627

Reads genomic origin

Exonic: 69,070,285 / 91.26%
Intronic: 3,632,231 / 4.8%
Intergenic: 2,983,452 / 3.94%
Intronic/intergenic overlapping exon: 2,537,455 / 3.35%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.21
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 21,507,510
ACCT 5.44%
AGGT 4.7%
TCCT 3.66%
ATCT 3.63%
AGGA 3.36%
GCCT 3.21%
AGCT 2.64%
AGGC 2.43%
CCCT 2.42%
TTCT 2.14%
AGAT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis