Input data and parameters 

Input

Analysis date: Mon Oct 30 23:07:16 GMT 2023
BAM file: SRX7354241.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): 42,597,475 / 42,560,026
Number of aligned pairs (without duplicates): 42,546,347
Total number of alignments: 92,455,458
Number of secondary alignments: 7,297,957
Number of non-unique alignments: 12,056,572
Aligned to genes: 72,876,762
Ambiguous alignments: 257,677
No feature assigned: 6,720,863
Missing chromosome in annotation: 543,584
Not aligned: 4,287,993

Reads genomic origin

Exonic: 72,876,762 / 91.56%
Intronic: 3,984,833 / 5.01%
Intergenic: 2,736,030 / 3.44%
Intronic/intergenic overlapping exon: 3,231,059 / 4.06%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.12
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 22,680,192
AGGT 5.24%
ACCT 4.95%
TCCT 3.9%
AGGA 3.57%
ATCT 3.51%
CCCT 2.64%
AGGC 2.52%
AGCT 2.15%
TTCT 2.1%
AGAA 2.05%
GCCT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis