Input data and parameters 

Input

Analysis date: Sun Oct 29 03:02:24 GMT 2023
BAM file: SRX7354167.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): 27,184,429 / 27,169,038
Number of aligned pairs (without duplicates): 27,165,458
Total number of alignments: 57,747,406
Number of secondary alignments: 3,393,939
Number of non-unique alignments: 5,347,993
Aligned to genes: 45,421,498
Ambiguous alignments: 149,784
No feature assigned: 6,461,483
Missing chromosome in annotation: 366,648
Not aligned: 3,282,499

Reads genomic origin

Exonic: 45,421,498 / 87.55%
Intronic: 4,005,263 / 7.72%
Intergenic: 2,456,220 / 4.73%
Intronic/intergenic overlapping exon: 2,028,546 / 3.91%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.23
5'-3' bias: 1.66

Junction analysis

Reads at junctions: 13,495,509
ACCT 5.63%
AGGT 4.49%
ATCT 3.92%
TCCT 3.85%
AGGA 3.27%
GCCT 3.24%
AGCT 2.61%
CCCT 2.59%
AGGC 2.36%
AGAT 2.04%
TTCT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis