Input data and parameters 

Input

Analysis date: Tue Oct 31 09:40:48 GMT 2023
BAM file: SRX7354290.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): 68,050,532 / 67,902,973
Number of aligned pairs (without duplicates): 67,877,470
Total number of alignments: 144,850,083
Number of secondary alignments: 8,896,578
Number of non-unique alignments: 14,898,420
Aligned to genes: 109,555,403
Ambiguous alignments: 386,893
No feature assigned: 19,479,841
Missing chromosome in annotation: 529,526
Not aligned: 11,679,931

Reads genomic origin

Exonic: 109,555,403 / 84.9%
Intronic: 14,091,275 / 10.92%
Intergenic: 5,388,566 / 4.18%
Intronic/intergenic overlapping exon: 5,575,202 / 4.32%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.15
5'-3' bias: 1.72

Junction analysis

Reads at junctions: 36,333,533
ACCT 5.44%
AGGT 4.71%
AGGA 3.66%
ATCT 3.6%
TCCT 3.31%
GCCT 3.08%
AGCT 2.66%
AGAT 2.5%
CCCT 2.37%
AGGC 2.36%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis