Input data and parameters 

Input

Analysis date: Sun Oct 29 01:49:30 GMT 2023
BAM file: SRX7354160.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): 37,000,964 / 36,979,190
Number of aligned pairs (without duplicates): 36,975,951
Total number of alignments: 79,722,844
Number of secondary alignments: 5,742,690
Number of non-unique alignments: 9,644,916
Aligned to genes: 63,442,726
Ambiguous alignments: 215,484
No feature assigned: 5,955,001
Missing chromosome in annotation: 464,717
Not aligned: 1,950,284

Reads genomic origin

Exonic: 63,442,726 / 91.42%
Intronic: 3,350,823 / 4.83%
Intergenic: 2,604,178 / 3.75%
Intronic/intergenic overlapping exon: 2,473,623 / 3.56%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.21
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 21,100,754
ACCT 5.51%
AGGT 4.51%
ATCT 3.54%
GCCT 3.51%
TCCT 3.47%
AGGA 3.35%
AGCT 2.63%
AGGC 2.33%
CCCT 2.29%
TTCT 2.11%
AGAT 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis