Input data and parameters 

Input

Analysis date: Sun Oct 29 01:25:49 GMT 2023
BAM file: SRX7354120.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): 34,162,043 / 34,124,206
Number of aligned pairs (without duplicates): 34,119,872
Total number of alignments: 72,676,831
Number of secondary alignments: 4,390,582
Number of non-unique alignments: 7,425,841
Aligned to genes: 56,537,285
Ambiguous alignments: 180,774
No feature assigned: 8,249,034
Missing chromosome in annotation: 283,897
Not aligned: 6,625,723

Reads genomic origin

Exonic: 56,537,285 / 87.27%
Intronic: 4,845,094 / 7.48%
Intergenic: 3,403,940 / 5.25%
Intronic/intergenic overlapping exon: 2,333,272 / 3.6%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.24
5'-3' bias: 2

Junction analysis

Reads at junctions: 17,009,269
ACCT 5.28%
AGGT 4.83%
AGGA 3.65%
ATCT 3.56%
TCCT 3.52%
GCCT 2.9%
AGCT 2.76%
CCCT 2.43%
AGGC 2.41%
AGAT 2.32%
TTCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis