Input data and parameters 

Input

Analysis date: Sun Oct 29 11:28:00 GMT 2023
BAM file: SRX7354078.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): 41,877,628 / 41,860,470
Number of aligned pairs (without duplicates): 41,849,209
Total number of alignments: 89,570,424
Number of secondary alignments: 5,832,326
Number of non-unique alignments: 9,407,928
Aligned to genes: 71,624,947
Ambiguous alignments: 239,266
No feature assigned: 7,744,382
Missing chromosome in annotation: 553,901
Not aligned: 2,623,862

Reads genomic origin

Exonic: 71,624,947 / 90.24%
Intronic: 4,815,318 / 6.07%
Intergenic: 2,929,064 / 3.69%
Intronic/intergenic overlapping exon: 2,970,831 / 3.74%

Transcript coverage profile

5' bias: 0.21
3' bias: 0.17
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 22,607,454
ACCT 5.51%
ATCT 4.43%
AGGT 4.4%
TCCT 4.01%
GCCT 3.44%
AGGA 3.14%
CCCT 2.67%
AGCT 2.26%
AGGC 2.18%
TTCT 2.1%
TCCC 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