Input data and parameters 

Input

Analysis date: Sun Oct 29 12:20:35 GMT 2023
BAM file: SRX7354119.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): 56,239,703 / 56,178,094
Number of aligned pairs (without duplicates): 56,171,379
Total number of alignments: 119,432,590
Number of secondary alignments: 7,014,793
Number of non-unique alignments: 11,549,460
Aligned to genes: 91,479,087
Ambiguous alignments: 293,944
No feature assigned: 15,503,741
Missing chromosome in annotation: 606,358
Not aligned: 8,841,247

Reads genomic origin

Exonic: 91,479,087 / 85.51%
Intronic: 10,161,947 / 9.5%
Intergenic: 5,341,794 / 4.99%
Intronic/intergenic overlapping exon: 3,834,238 / 3.58%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.17
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 26,477,875
ACCT 5.49%
AGGT 4.81%
ATCT 3.84%
AGGA 3.59%
TCCT 3.38%
GCCT 3.31%
AGCT 2.63%
CCCT 2.56%
AGGC 2.43%
AGAT 2.3%
TTCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis