Input data and parameters 

Input

Analysis date: Mon Oct 30 22:56:47 GMT 2023
BAM file: SRX7354215.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): 35,236,109 / 35,216,179
Number of aligned pairs (without duplicates): 35,211,699
Total number of alignments: 74,819,370
Number of secondary alignments: 4,367,082
Number of non-unique alignments: 7,124,971
Aligned to genes: 57,450,195
Ambiguous alignments: 187,156
No feature assigned: 9,669,543
Missing chromosome in annotation: 387,505
Not aligned: 3,278,352

Reads genomic origin

Exonic: 57,450,195 / 85.59%
Intronic: 6,841,838 / 10.19%
Intergenic: 2,827,705 / 4.21%
Intronic/intergenic overlapping exon: 2,366,734 / 3.53%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.15
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 17,933,348
ACCT 5.24%
AGGT 4.72%
AGGA 3.75%
ATCT 3.62%
TCCT 3.32%
AGCT 2.8%
GCCT 2.79%
AGAT 2.55%
AGGC 2.37%
CCCT 2.3%
TTCT 2.28%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis