Input data and parameters 

Input

Analysis date: Tue Oct 31 09:26:42 GMT 2023
BAM file: SRX7354309.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): 38,648,215 / 38,624,577
Number of aligned pairs (without duplicates): 38,621,994
Total number of alignments: 82,481,459
Number of secondary alignments: 5,208,667
Number of non-unique alignments: 8,459,072
Aligned to genes: 64,561,136
Ambiguous alignments: 238,311
No feature assigned: 8,809,143
Missing chromosome in annotation: 413,797
Not aligned: 1,853,064

Reads genomic origin

Exonic: 64,561,136 / 87.99%
Intronic: 6,167,367 / 8.41%
Intergenic: 2,641,776 / 3.6%
Intronic/intergenic overlapping exon: 2,247,279 / 3.06%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.22
5'-3' bias: 2.03

Junction analysis

Reads at junctions: 20,588,908
ACCT 5.26%
AGGT 4.76%
ATCT 3.62%
AGGA 3.59%
TCCT 3.42%
GCCT 3.15%
AGCT 2.71%
CCCT 2.56%
AGAT 2.37%
AGGC 2.36%
TTCT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis