Input data and parameters 

Input

Analysis date: Tue Oct 31 01:11:53 GMT 2023
BAM file: SRX7354266.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): 28,143,212 / 28,129,061
Number of aligned pairs (without duplicates): 28,127,383
Total number of alignments: 59,965,308
Number of secondary alignments: 3,693,035
Number of non-unique alignments: 6,163,320
Aligned to genes: 46,711,974
Ambiguous alignments: 157,367
No feature assigned: 6,676,428
Missing chromosome in annotation: 256,219
Not aligned: 1,250,291

Reads genomic origin

Exonic: 46,711,974 / 87.49%
Intronic: 4,314,540 / 8.08%
Intergenic: 2,361,888 / 4.42%
Intronic/intergenic overlapping exon: 1,784,953 / 3.34%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.2
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 14,102,502
ACCT 5.3%
AGGT 4.85%
AGGA 3.7%
ATCT 3.59%
TCCT 3.38%
GCCT 2.89%
AGCT 2.8%
AGAT 2.43%
CCCT 2.41%
AGGC 2.39%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis