Input data and parameters 

Input

Analysis date: Mon Oct 30 23:35:59 GMT 2023
BAM file: SRX7354242.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): 65,926,347 / 65,890,423
Number of aligned pairs (without duplicates): 65,878,050
Total number of alignments: 142,754,241
Number of secondary alignments: 10,937,471
Number of non-unique alignments: 16,920,087
Aligned to genes: 112,579,920
Ambiguous alignments: 559,353
No feature assigned: 11,290,516
Missing chromosome in annotation: 1,404,365
Not aligned: 6,626,484

Reads genomic origin

Exonic: 112,579,920 / 90.89%
Intronic: 5,675,082 / 4.58%
Intergenic: 5,615,434 / 4.53%
Intronic/intergenic overlapping exon: 5,488,616 / 4.43%

Transcript coverage profile

5' bias: 0.13
3' bias: 0.13
5'-3' bias: 2.21

Junction analysis

Reads at junctions: 43,454,013
TCCT 5.25%
ACCT 4.9%
ATCT 4.55%
AGGT 4.38%
CCCT 3.6%
AGGA 2.93%
AGGC 2.5%
GCCT 2.3%
AGAC 2.12%
TTCT 2.02%
AGCT 2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis