Input data and parameters 

Input

Analysis date: Sun Oct 29 01:48:42 GMT 2023
BAM file: SRX7354157.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): 37,416,554 / 37,380,459
Number of aligned pairs (without duplicates): 37,376,452
Total number of alignments: 79,494,439
Number of secondary alignments: 4,697,426
Number of non-unique alignments: 7,798,287
Aligned to genes: 63,881,160
Ambiguous alignments: 221,293
No feature assigned: 7,274,929
Missing chromosome in annotation: 318,770
Not aligned: 4,679,217

Reads genomic origin

Exonic: 63,881,160 / 89.78%
Intronic: 4,673,302 / 6.57%
Intergenic: 2,601,627 / 3.66%
Intronic/intergenic overlapping exon: 2,283,841 / 3.21%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.15
5'-3' bias: 2.32

Junction analysis

Reads at junctions: 19,322,187
ACCT 5.46%
AGGT 4.73%
ATCT 3.57%
TCCT 3.5%
AGGA 3.47%
GCCT 2.92%
TTCT 2.74%
AGCT 2.6%
AGGC 2.4%
CCCT 2.29%
AGAT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis