Input data and parameters 

Input

Analysis date: Tue Oct 31 14:11:54 GMT 2023
BAM file: SRX7354386.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): 66,895,681 / 66,857,980
Number of aligned pairs (without duplicates): 66,849,125
Total number of alignments: 144,113,613
Number of secondary alignments: 10,359,952
Number of non-unique alignments: 16,946,433
Aligned to genes: 113,868,354
Ambiguous alignments: 515,524
No feature assigned: 11,959,955
Missing chromosome in annotation: 823,347
Not aligned: 3,763,335

Reads genomic origin

Exonic: 113,868,354 / 90.5%
Intronic: 8,023,914 / 6.38%
Intergenic: 3,936,041 / 3.13%
Intronic/intergenic overlapping exon: 4,952,816 / 3.94%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.23
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 39,083,663
ACCT 5.43%
AGGT 4.39%
TCCT 4.12%
ATCT 4.09%
GCCT 3.58%
AGGA 3.08%
CCCT 2.84%
AGCT 2.3%
AGGC 2.23%
TTCT 2.18%
TCCC 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