Input data and parameters 

Input

Analysis date: Mon Oct 30 20:15:34 GMT 2023
BAM file: SRX7354217.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): 27,974,458 / 27,965,686
Number of aligned pairs (without duplicates): 27,964,013
Total number of alignments: 59,592,577
Number of secondary alignments: 3,652,433
Number of non-unique alignments: 5,906,644
Aligned to genes: 46,545,332
Ambiguous alignments: 158,744
No feature assigned: 6,591,651
Missing chromosome in annotation: 390,206
Not aligned: 881,478

Reads genomic origin

Exonic: 46,545,332 / 87.59%
Intronic: 3,610,375 / 6.79%
Intergenic: 2,981,276 / 5.61%
Intronic/intergenic overlapping exon: 1,850,262 / 3.48%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.28
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 15,938,000
ACCT 5%
AGGT 4.8%
TCCT 3.54%
AGGA 3.53%
ATCT 3.49%
GCCT 3.11%
AGCT 2.77%
CCCT 2.58%
AGGC 2.44%
TTCT 2.13%
AGAT 2.08%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis