Input data and parameters 

Input

Analysis date: Sun Oct 29 01:47:01 GMT 2023
BAM file: SRX7354066.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): 40,023,127 / 39,999,985
Number of aligned pairs (without duplicates): 39,997,496
Total number of alignments: 87,454,278
Number of secondary alignments: 7,431,166
Number of non-unique alignments: 12,993,793
Aligned to genes: 66,569,187
Ambiguous alignments: 176,801
No feature assigned: 7,340,379
Missing chromosome in annotation: 374,118
Not aligned: 1,643,388

Reads genomic origin

Exonic: 66,569,187 / 90.07%
Intronic: 4,089,167 / 5.53%
Intergenic: 3,251,212 / 4.4%
Intronic/intergenic overlapping exon: 2,082,097 / 2.82%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.14
5'-3' bias: 1.95

Junction analysis

Reads at junctions: 14,228,902
ACCT 5.14%
ATCT 4.69%
AGGT 4.24%
TCCT 3.8%
GCCT 3.39%
AGGA 3.27%
CCCT 2.91%
TTCT 2.48%
AGCT 2.25%
AGGC 2.12%
TCCC 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis