Input data and parameters 

Input

Analysis date: Tue Oct 31 09:46:56 GMT 2023
BAM file: SRX7354350.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): 36,264,754 / 36,238,511
Number of aligned pairs (without duplicates): 36,233,555
Total number of alignments: 77,738,377
Number of secondary alignments: 5,235,112
Number of non-unique alignments: 8,432,839
Aligned to genes: 59,945,597
Ambiguous alignments: 202,316
No feature assigned: 8,637,649
Missing chromosome in annotation: 519,976
Not aligned: 3,286,887

Reads genomic origin

Exonic: 59,945,597 / 87.41%
Intronic: 6,045,105 / 8.81%
Intergenic: 2,592,544 / 3.78%
Intronic/intergenic overlapping exon: 2,185,336 / 3.19%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.24
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 18,095,049
ACCT 5.31%
AGGT 4.65%
ATCT 3.6%
AGGA 3.46%
GCCT 3.42%
TCCT 3.38%
AGCT 2.72%
CCCT 2.52%
AGGC 2.36%
TTCT 2.32%
AGAT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis