Input data and parameters 

Input

Analysis date: Tue Oct 31 09:49:52 GMT 2023
BAM file: SRX7354366.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): 43,915,520 / 43,885,363
Number of aligned pairs (without duplicates): 43,877,800
Total number of alignments: 94,676,713
Number of secondary alignments: 6,875,830
Number of non-unique alignments: 11,024,144
Aligned to genes: 75,194,631
Ambiguous alignments: 324,076
No feature assigned: 7,471,814
Missing chromosome in annotation: 662,048
Not aligned: 2,364,129

Reads genomic origin

Exonic: 75,194,631 / 90.96%
Intronic: 4,572,447 / 5.53%
Intergenic: 2,899,367 / 3.51%
Intronic/intergenic overlapping exon: 3,373,207 / 4.08%

Transcript coverage profile

5' bias: 0.21
3' bias: 0.2
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 27,026,674
ACCT 5.26%
ATCT 4.95%
TCCT 4.82%
AGGT 4.15%
GCCT 3.37%
CCCT 3.09%
AGGA 2.93%
TTCT 2.28%
AGCT 2.21%
AGGC 2.06%
TCCC 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis