Input data and parameters 

Input

Analysis date: Sun Oct 29 02:27:51 GMT 2023
BAM file: SRX7354069.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): 56,342,109 / 56,318,118
Number of aligned pairs (without duplicates): 56,311,546
Total number of alignments: 120,771,362
Number of secondary alignments: 8,111,135
Number of non-unique alignments: 13,442,984
Aligned to genes: 94,332,928
Ambiguous alignments: 339,189
No feature assigned: 12,013,333
Missing chromosome in annotation: 642,928
Not aligned: 2,962,341

Reads genomic origin

Exonic: 94,332,928 / 88.7%
Intronic: 8,642,927 / 8.13%
Intergenic: 3,370,406 / 3.17%
Intronic/intergenic overlapping exon: 4,103,193 / 3.86%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.17
5'-3' bias: 1.91

Junction analysis

Reads at junctions: 31,293,488
ACCT 5.4%
AGGT 4.67%
ATCT 3.66%
TCCT 3.49%
AGGA 3.44%
GCCT 3.19%
AGCT 2.62%
TTCT 2.45%
AGGC 2.4%
CCCT 2.37%
AGAT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis