Input data and parameters 

Input

Analysis date: Tue Oct 31 01:12:57 GMT 2023
BAM file: SRX7354269.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): 34,884,078 / 34,870,025
Number of aligned pairs (without duplicates): 34,866,999
Total number of alignments: 74,741,199
Number of secondary alignments: 4,987,096
Number of non-unique alignments: 7,684,640
Aligned to genes: 57,287,424
Ambiguous alignments: 199,215
No feature assigned: 8,863,934
Missing chromosome in annotation: 705,986
Not aligned: 1,688,861

Reads genomic origin

Exonic: 57,287,424 / 86.6%
Intronic: 4,992,328 / 7.55%
Intergenic: 3,871,606 / 5.85%
Intronic/intergenic overlapping exon: 2,251,901 / 3.4%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.27
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 18,958,295
AGGT 4.99%
ACCT 4.98%
AGGA 3.6%
TCCT 3.4%
ATCT 3.32%
GCCT 2.88%
AGCT 2.85%
AGGC 2.51%
CCCT 2.45%
AGAT 2.17%
TTCT 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis