Input data and parameters 

Input

Analysis date: Tue Oct 31 09:28:23 GMT 2023
BAM file: SRX7354272.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): 47,844,298 / 47,826,216
Number of aligned pairs (without duplicates): 47,822,259
Total number of alignments: 101,729,709
Number of secondary alignments: 6,059,195
Number of non-unique alignments: 9,828,113
Aligned to genes: 76,237,853
Ambiguous alignments: 264,309
No feature assigned: 14,806,915
Missing chromosome in annotation: 592,519
Not aligned: 2,363,440

Reads genomic origin

Exonic: 76,237,853 / 83.74%
Intronic: 7,987,118 / 8.77%
Intergenic: 6,819,797 / 7.49%
Intronic/intergenic overlapping exon: 3,175,289 / 3.49%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.24
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 25,716,422
ACCT 5%
AGGT 4.72%
ATCT 3.67%
TCCT 3.53%
AGGA 3.41%
GCCT 3.23%
AGCT 2.71%
CCCT 2.7%
AGGC 2.43%
TTCT 2.28%
AGAT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis