Input data and parameters 

Input

Analysis date: Sun Oct 29 01:40:18 GMT 2023
BAM file: SRX7354086.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): 34,872,588 / 34,842,289
Number of aligned pairs (without duplicates): 34,838,712
Total number of alignments: 74,179,474
Number of secondary alignments: 4,464,597
Number of non-unique alignments: 7,493,199
Aligned to genes: 59,860,018
Ambiguous alignments: 203,261
No feature assigned: 6,390,709
Missing chromosome in annotation: 232,287
Not aligned: 5,433,491

Reads genomic origin

Exonic: 59,860,018 / 90.35%
Intronic: 4,484,950 / 6.77%
Intergenic: 1,905,759 / 2.88%
Intronic/intergenic overlapping exon: 2,069,530 / 3.12%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.19
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 22,134,805
ACCT 5.29%
AGGT 5.03%
AGGA 3.69%
TCCT 3.62%
ATCT 3.61%
AGCT 2.83%
AGGC 2.44%
GCCT 2.4%
CCCT 2.26%
AGAT 2.18%
AGGG 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