Input data and parameters 

Input

Analysis date: Mon Oct 30 11:48:12 GMT 2023
BAM file: SRX7354181.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): 50,691,717 / 50,649,246
Number of aligned pairs (without duplicates): 50,636,319
Total number of alignments: 109,071,547
Number of secondary alignments: 7,730,584
Number of non-unique alignments: 12,188,282
Aligned to genes: 86,655,448
Ambiguous alignments: 307,759
No feature assigned: 9,035,260
Missing chromosome in annotation: 884,798
Not aligned: 6,529,587

Reads genomic origin

Exonic: 86,655,448 / 90.56%
Intronic: 5,169,163 / 5.4%
Intergenic: 3,866,097 / 4.04%
Intronic/intergenic overlapping exon: 3,564,266 / 3.72%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.21
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 24,993,748
ACCT 5.28%
AGGT 4.7%
ATCT 4.14%
TCCT 4.07%
AGGA 3.29%
GCCT 3.17%
CCCT 2.83%
AGCT 2.4%
AGGC 2.23%
TTCT 2.22%
AGAA 1.98%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis