Input data and parameters 

Input

Analysis date: Sun Oct 29 02:04:53 GMT 2023
BAM file: SRX7354073.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): 41,137,377 / 41,110,579
Number of aligned pairs (without duplicates): 41,107,353
Total number of alignments: 88,043,530
Number of secondary alignments: 5,795,574
Number of non-unique alignments: 9,455,229
Aligned to genes: 68,641,636
Ambiguous alignments: 254,839
No feature assigned: 9,340,537
Missing chromosome in annotation: 351,289
Not aligned: 2,753,522

Reads genomic origin

Exonic: 68,641,636 / 88.02%
Intronic: 7,474,021 / 9.58%
Intergenic: 1,866,516 / 2.39%
Intronic/intergenic overlapping exon: 2,443,085 / 3.13%

Transcript coverage profile

5' bias: 0.4
3' bias: 0.2
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 25,364,238
ACCT 5.06%
AGGT 4.3%
AGGG 3.44%
AGGA 3.31%
TCCT 3.13%
ATCT 3.11%
AGCT 2.51%
CCCT 2.49%
GCCT 2.25%
AGGC 2.09%
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