Input data and parameters 

Input

Analysis date: Sun Oct 29 12:29:42 GMT 2023
BAM file: SRX7354139.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): 45,552,438 / 45,501,949
Number of aligned pairs (without duplicates): 45,484,368
Total number of alignments: 100,178,578
Number of secondary alignments: 9,124,191
Number of non-unique alignments: 12,406,841
Aligned to genes: 75,484,425
Ambiguous alignments: 258,981
No feature assigned: 10,003,424
Missing chromosome in annotation: 2,024,907
Not aligned: 2,756,487

Reads genomic origin

Exonic: 75,484,425 / 88.3%
Intronic: 6,365,459 / 7.45%
Intergenic: 3,637,965 / 4.26%
Intronic/intergenic overlapping exon: 3,619,864 / 4.23%

Transcript coverage profile

5' bias: 0.52
3' bias: 0.22
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 23,174,917
ACCT 5.1%
AGGT 4.84%
ATCT 3.59%
TCCT 3.49%
AGGA 3.42%
GCCT 3.31%
CCCT 2.87%
AGCT 2.76%
AGGC 2.52%
TTCT 2.25%
AGAT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis