Input data and parameters 

Input

Analysis date: Mon Oct 30 23:20:47 GMT 2023
BAM file: SRX7354221.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): 36,503,748 / 36,481,069
Number of aligned pairs (without duplicates): 36,477,526
Total number of alignments: 77,082,466
Number of secondary alignments: 4,097,649
Number of non-unique alignments: 6,695,566
Aligned to genes: 60,699,706
Ambiguous alignments: 223,256
No feature assigned: 9,153,955
Missing chromosome in annotation: 309,983
Not aligned: 3,474,061

Reads genomic origin

Exonic: 60,699,706 / 86.9%
Intronic: 6,317,388 / 9.04%
Intergenic: 2,836,567 / 4.06%
Intronic/intergenic overlapping exon: 2,454,342 / 3.51%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.18
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 19,739,845
ACCT 5.43%
AGGT 4.8%
AGGA 3.59%
ATCT 3.55%
TCCT 3.37%
GCCT 3.06%
AGCT 2.78%
AGGC 2.44%
CCCT 2.35%
AGAT 2.29%
TTCT 2.27%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis