Input data and parameters 

Input

Analysis date: Mon Oct 30 12:46:59 GMT 2023
BAM file: SRX7354212.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): 37,942,763 / 37,933,733
Number of aligned pairs (without duplicates): 37,930,542
Total number of alignments: 80,868,024
Number of secondary alignments: 4,991,528
Number of non-unique alignments: 8,258,805
Aligned to genes: 63,934,321
Ambiguous alignments: 214,149
No feature assigned: 8,095,208
Missing chromosome in annotation: 365,541
Not aligned: 1,442,106

Reads genomic origin

Exonic: 63,934,321 / 88.76%
Intronic: 5,163,269 / 7.17%
Intergenic: 2,931,939 / 4.07%
Intronic/intergenic overlapping exon: 2,154,000 / 2.99%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.17
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 19,757,900
ACCT 5.56%
AGGT 4.78%
AGGA 3.52%
ATCT 3.49%
GCCT 3.28%
TCCT 3.26%
AGCT 2.77%
AGGC 2.41%
AGAT 2.3%
CCCT 2.29%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis