Input data and parameters 

Input

Analysis date: Tue Oct 31 09:46:24 GMT 2023
BAM file: SRX7354355.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): 37,924,481 / 37,900,771
Number of aligned pairs (without duplicates): 37,897,593
Total number of alignments: 80,698,360
Number of secondary alignments: 4,873,108
Number of non-unique alignments: 8,289,965
Aligned to genes: 62,889,147
Ambiguous alignments: 211,817
No feature assigned: 9,044,281
Missing chromosome in annotation: 263,150
Not aligned: 3,767,248

Reads genomic origin

Exonic: 62,889,147 / 87.43%
Intronic: 5,704,834 / 7.93%
Intergenic: 3,339,447 / 4.64%
Intronic/intergenic overlapping exon: 2,402,038 / 3.34%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.16
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 19,111,827
ACCT 5.24%
AGGT 4.74%
ATCT 3.74%
AGGA 3.63%
TCCT 3.38%
GCCT 3.17%
AGCT 2.66%
CCCT 2.44%
AGGC 2.37%
AGAT 2.31%
TTCT 2.27%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis