Input data and parameters 

Input

Analysis date: Tue Oct 31 01:11:58 GMT 2023
BAM file: SRX7354275.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): 38,745,906 / 38,727,893
Number of aligned pairs (without duplicates): 38,724,558
Total number of alignments: 81,724,604
Number of secondary alignments: 4,250,805
Number of non-unique alignments: 7,169,348
Aligned to genes: 65,205,167
Ambiguous alignments: 211,388
No feature assigned: 8,855,449
Missing chromosome in annotation: 283,252
Not aligned: 3,045,629

Reads genomic origin

Exonic: 65,205,167 / 88.04%
Intronic: 5,370,701 / 7.25%
Intergenic: 3,484,748 / 4.71%
Intronic/intergenic overlapping exon: 2,623,014 / 3.54%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.15
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 20,231,531
ACCT 5.49%
AGGT 4.77%
AGGA 3.6%
ATCT 3.55%
TCCT 3.28%
GCCT 3.18%
AGCT 2.78%
AGGC 2.4%
AGAT 2.32%
CCCT 2.32%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis