Input data and parameters 

Input

Analysis date: Tue Oct 31 01:30:23 GMT 2023
BAM file: SRX7354279.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): 46,172,871 / 46,099,030
Number of aligned pairs (without duplicates): 46,093,401
Total number of alignments: 100,905,897
Number of secondary alignments: 8,633,996
Number of non-unique alignments: 11,029,229
Aligned to genes: 72,445,730
Ambiguous alignments: 382,782
No feature assigned: 15,083,611
Missing chromosome in annotation: 1,964,545
Not aligned: 4,694,751

Reads genomic origin

Exonic: 72,445,730 / 82.77%
Intronic: 12,974,879 / 14.82%
Intergenic: 2,108,732 / 2.41%
Intronic/intergenic overlapping exon: 3,196,992 / 3.65%

Transcript coverage profile

5' bias: 0.4
3' bias: 0.23
5'-3' bias: 1.64

Junction analysis

Reads at junctions: 33,014,458
ACCT 5%
AGGT 4.65%
ATCT 3.77%
AGGA 3.66%
TCCT 3.5%
GCCT 3.11%
AGCT 2.74%
CCCT 2.73%
AGGC 2.37%
TTCT 2.26%
AGAT 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