Input data and parameters 

Input

Analysis date: Mon Oct 30 12:57:14 GMT 2023
BAM file: SRX7354205.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): 36,785,659 / 36,758,523
Number of aligned pairs (without duplicates): 36,754,907
Total number of alignments: 79,060,583
Number of secondary alignments: 5,516,401
Number of non-unique alignments: 8,737,387
Aligned to genes: 55,012,156
Ambiguous alignments: 202,650
No feature assigned: 14,466,301
Missing chromosome in annotation: 642,089
Not aligned: 3,749,026

Reads genomic origin

Exonic: 55,012,156 / 79.18%
Intronic: 7,805,722 / 11.23%
Intergenic: 6,660,579 / 9.59%
Intronic/intergenic overlapping exon: 2,372,250 / 3.41%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.24
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 21,362,368
ACCT 5.17%
AGGT 4.64%
ATCT 3.65%
TCCT 3.6%
GCCT 3.49%
AGGA 3.45%
CCCT 2.86%
AGCT 2.74%
AGGC 2.39%
TTCT 2.3%
AGAT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis