Input data and parameters 

Input

Analysis date: Tue Oct 31 13:23:43 GMT 2023
BAM file: SRX7354186.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): 36,981,862 / 36,963,434
Number of aligned pairs (without duplicates): 36,960,146
Total number of alignments: 78,337,454
Number of secondary alignments: 4,392,158
Number of non-unique alignments: 7,327,110
Aligned to genes: 63,624,762
Ambiguous alignments: 230,641
No feature assigned: 6,862,128
Missing chromosome in annotation: 292,813
Not aligned: 4,665,224

Reads genomic origin

Exonic: 63,624,762 / 90.26%
Intronic: 4,222,133 / 5.99%
Intergenic: 2,639,995 / 3.75%
Intronic/intergenic overlapping exon: 2,305,691 / 3.27%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.16
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 21,008,843
ACCT 5.67%
AGGT 4.6%
ATCT 3.76%
TCCT 3.59%
GCCT 3.35%
AGGA 3.3%
AGCT 2.58%
CCCT 2.35%
AGGC 2.33%
TTCT 2.06%
AGAT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis