Input data and parameters 

Input

Analysis date: Mon Oct 30 22:25:44 GMT 2023
BAM file: SRX7354263.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): 31,739,100 / 31,702,146
Number of aligned pairs (without duplicates): 31,691,248
Total number of alignments: 67,886,239
Number of secondary alignments: 4,444,993
Number of non-unique alignments: 7,157,317
Aligned to genes: 54,084,209
Ambiguous alignments: 182,103
No feature assigned: 6,010,572
Missing chromosome in annotation: 452,038
Not aligned: 5,614,372

Reads genomic origin

Exonic: 54,084,209 / 90%
Intronic: 3,363,418 / 5.6%
Intergenic: 2,647,154 / 4.4%
Intronic/intergenic overlapping exon: 2,202,253 / 3.66%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.19
5'-3' bias: 2.13

Junction analysis

Reads at junctions: 17,883,484
ACCT 5.44%
AGGT 4.66%
ATCT 3.62%
TCCT 3.58%
AGGA 3.43%
GCCT 3.12%
AGCT 2.69%
AGGC 2.4%
CCCT 2.36%
TTCT 2.24%
AGAT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis