Input data and parameters 

Input

Analysis date: Mon Oct 30 09:38:59 GMT 2023
BAM file: SRX7354207.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): 42,232,833 / 42,208,619
Number of aligned pairs (without duplicates): 42,200,447
Total number of alignments: 89,788,179
Number of secondary alignments: 5,346,727
Number of non-unique alignments: 8,264,363
Aligned to genes: 69,071,347
Ambiguous alignments: 236,738
No feature assigned: 11,547,647
Missing chromosome in annotation: 668,084
Not aligned: 2,097,226

Reads genomic origin

Exonic: 69,071,347 / 85.68%
Intronic: 8,224,162 / 10.2%
Intergenic: 3,323,485 / 4.12%
Intronic/intergenic overlapping exon: 3,245,592 / 4.03%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.17
5'-3' bias: 2.07

Junction analysis

Reads at junctions: 22,830,658
ACCT 5.41%
AGGT 4.78%
AGGA 3.57%
ATCT 3.53%
GCCT 3.32%
TCCT 3.29%
AGCT 2.7%
AGGC 2.42%
CCCT 2.33%
AGAT 2.29%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis