Input data and parameters 

Input

Analysis date: Mon Oct 30 20:30:08 GMT 2023
BAM file: SRX7354249.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): 31,585,753 / 31,558,365
Number of aligned pairs (without duplicates): 31,547,007
Total number of alignments: 68,219,661
Number of secondary alignments: 5,075,543
Number of non-unique alignments: 7,991,039
Aligned to genes: 52,906,605
Ambiguous alignments: 242,653
No feature assigned: 6,524,392
Missing chromosome in annotation: 554,972
Not aligned: 1,485,008

Reads genomic origin

Exonic: 52,906,605 / 89.02%
Intronic: 4,419,013 / 7.44%
Intergenic: 2,105,379 / 3.54%
Intronic/intergenic overlapping exon: 2,993,674 / 5.04%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.23
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 19,088,914
ACCT 4.99%
AGGT 4.7%
ATCT 4.08%
TCCT 4.01%
AGGA 3.19%
CCCT 3.03%
GCCT 2.86%
AGGC 2.48%
AGCT 2.41%
TTCT 2.1%
AGAA 1.88%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis