Input data and parameters 

Input

Analysis date: Sun Oct 29 01:42:07 GMT 2023
BAM file: SRX7354057.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): 37,022,810 / 36,993,632
Number of aligned pairs (without duplicates): 36,990,630
Total number of alignments: 79,346,136
Number of secondary alignments: 5,329,694
Number of non-unique alignments: 8,852,599
Aligned to genes: 61,068,937
Ambiguous alignments: 249,758
No feature assigned: 8,806,684
Missing chromosome in annotation: 368,158
Not aligned: 2,353,108

Reads genomic origin

Exonic: 61,068,937 / 87.4%
Intronic: 6,477,740 / 9.27%
Intergenic: 2,328,944 / 3.33%
Intronic/intergenic overlapping exon: 2,471,330 / 3.54%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.24
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 22,097,158
ACCT 5.34%
AGGT 4.61%
ATCT 3.45%
TCCT 3.45%
GCCT 3.44%
AGGA 3.4%
AGCT 2.77%
CCCT 2.47%
AGGC 2.37%
AGAT 2.2%
TTCT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis