Input data and parameters 

Input

Analysis date: Tue Oct 31 09:52:26 GMT 2023
BAM file: SRX7354361.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): 26,929,969 / 26,913,475
Number of aligned pairs (without duplicates): 26,911,681
Total number of alignments: 57,201,849
Number of secondary alignments: 3,358,405
Number of non-unique alignments: 5,703,861
Aligned to genes: 44,822,964
Ambiguous alignments: 155,899
No feature assigned: 6,341,256
Missing chromosome in annotation: 177,869
Not aligned: 1,221,126

Reads genomic origin

Exonic: 44,822,964 / 87.61%
Intronic: 4,420,807 / 8.64%
Intergenic: 1,920,449 / 3.75%
Intronic/intergenic overlapping exon: 1,713,221 / 3.35%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.22
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 14,353,434
ACCT 5.27%
AGGT 4.6%
ATCT 3.74%
TCCT 3.54%
AGGA 3.53%
GCCT 3.23%
AGCT 2.71%
CCCT 2.47%
AGGC 2.36%
AGAT 2.24%
TTCT 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