Input data and parameters 

Input

Analysis date: Sun Oct 29 12:51:51 GMT 2023
BAM file: SRX7354161.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): 34,191,465 / 34,171,478
Number of aligned pairs (without duplicates): 34,167,863
Total number of alignments: 72,666,331
Number of secondary alignments: 4,303,388
Number of non-unique alignments: 6,893,391
Aligned to genes: 58,001,234
Ambiguous alignments: 209,823
No feature assigned: 7,149,163
Missing chromosome in annotation: 412,720
Not aligned: 1,784,577

Reads genomic origin

Exonic: 58,001,234 / 89.03%
Intronic: 5,085,272 / 7.81%
Intergenic: 2,063,891 / 3.17%
Intronic/intergenic overlapping exon: 2,083,076 / 3.2%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.22
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 19,090,308
ACCT 5.32%
AGGT 4.56%
ATCT 3.61%
TCCT 3.55%
AGGA 3.37%
GCCT 3.36%
AGCT 2.68%
CCCT 2.44%
TTCT 2.34%
AGGC 2.32%
AGAT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis