Input data and parameters 

Input

Analysis date: Tue Oct 31 09:50:39 GMT 2023
BAM file: SRX7354378.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): 31,509,835 / 31,488,128
Number of aligned pairs (without duplicates): 31,484,352
Total number of alignments: 66,851,293
Number of secondary alignments: 3,853,330
Number of non-unique alignments: 6,258,286
Aligned to genes: 51,773,257
Ambiguous alignments: 174,767
No feature assigned: 8,315,266
Missing chromosome in annotation: 329,717
Not aligned: 2,825,283

Reads genomic origin

Exonic: 51,773,257 / 86.16%
Intronic: 5,801,773 / 9.66%
Intergenic: 2,513,493 / 4.18%
Intronic/intergenic overlapping exon: 2,111,905 / 3.51%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.22
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 16,724,217
ACCT 5.33%
AGGT 4.72%
ATCT 3.59%
AGGA 3.52%
TCCT 3.27%
GCCT 3.2%
AGCT 2.83%
AGGC 2.43%
CCCT 2.39%
AGAT 2.32%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis