Input data and parameters 

Input

Analysis date: Tue Oct 31 09:35:33 GMT 2023
BAM file: SRX7354340.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): 38,571,961 / 38,542,026
Number of aligned pairs (without duplicates): 38,538,312
Total number of alignments: 82,483,363
Number of secondary alignments: 5,369,376
Number of non-unique alignments: 8,869,599
Aligned to genes: 66,456,211
Ambiguous alignments: 269,011
No feature assigned: 6,484,329
Missing chromosome in annotation: 404,213
Not aligned: 5,625,105

Reads genomic origin

Exonic: 66,456,211 / 91.11%
Intronic: 3,723,038 / 5.1%
Intergenic: 2,761,291 / 3.79%
Intronic/intergenic overlapping exon: 2,405,398 / 3.3%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.21
5'-3' bias: 1.64

Junction analysis

Reads at junctions: 20,684,999
ACCT 5.43%
AGGT 4.5%
ATCT 4.46%
TCCT 4.1%
GCCT 3.57%
CCCT 3.01%
AGGA 3.01%
AGCT 2.36%
TTCT 2.36%
AGGC 2.26%
AGAA 1.78%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis