Input data and parameters 

Input

Analysis date: Tue Oct 31 09:46:35 GMT 2023
BAM file: SRX7354354.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): 31,747,210 / 31,725,434
Number of aligned pairs (without duplicates): 31,720,308
Total number of alignments: 70,026,674
Number of secondary alignments: 6,554,030
Number of non-unique alignments: 8,632,244
Aligned to genes: 54,497,215
Ambiguous alignments: 233,717
No feature assigned: 5,214,594
Missing chromosome in annotation: 1,448,904
Not aligned: 3,049,144

Reads genomic origin

Exonic: 54,497,215 / 91.27%
Intronic: 3,008,902 / 5.04%
Intergenic: 2,205,692 / 3.69%
Intronic/intergenic overlapping exon: 2,105,165 / 3.53%

Transcript coverage profile

5' bias: 0.18
3' bias: 0.18
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 17,886,771
ACCT 5.23%
TCCT 4.86%
ATCT 4.83%
AGGT 4.25%
CCCT 3.23%
AGGA 3.01%
GCCT 2.88%
TTCT 2.22%
AGCT 2.17%
AGGC 2.13%
GTCT 1.82%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis