Input data and parameters 

Input

Analysis date: Tue Oct 31 10:36:59 GMT 2023
BAM file: SRX7354297.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): 179,477,962 / 179,182,277
Number of aligned pairs (without duplicates): 179,130,875
Total number of alignments: 392,664,657
Number of secondary alignments: 34,004,418
Number of non-unique alignments: 41,113,842
Aligned to genes: 272,896,516
Ambiguous alignments: 1,281,608
No feature assigned: 68,383,258
Missing chromosome in annotation: 8,989,433
Not aligned: 14,198,237

Reads genomic origin

Exonic: 272,896,516 / 79.96%
Intronic: 60,072,824 / 17.6%
Intergenic: 8,310,434 / 2.44%
Intronic/intergenic overlapping exon: 15,755,018 / 4.62%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.17
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 112,639,441
ACCT 5.11%
AGGT 4.61%
ATCT 3.63%
AGGA 3.61%
TCCT 3.46%
GCCT 3.11%
AGCT 2.74%
CCCT 2.53%
AGGC 2.37%
AGAT 2.29%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis