Input data and parameters 

Input

Analysis date: Sun Oct 29 01:43:01 GMT 2023
BAM file: SRX7354059.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): 32,044,222 / 32,024,451
Number of aligned pairs (without duplicates): 32,020,437
Total number of alignments: 68,564,599
Number of secondary alignments: 4,495,926
Number of non-unique alignments: 6,961,804
Aligned to genes: 48,844,279
Ambiguous alignments: 202,013
No feature assigned: 12,065,261
Missing chromosome in annotation: 491,242
Not aligned: 1,752,511

Reads genomic origin

Exonic: 48,844,279 / 80.19%
Intronic: 10,083,901 / 16.56%
Intergenic: 1,981,360 / 3.25%
Intronic/intergenic overlapping exon: 2,411,238 / 3.96%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.22
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 18,129,667
ACCT 5.34%
AGGT 4.59%
ATCT 3.62%
TCCT 3.56%
AGGA 3.48%
GCCT 3.06%
AGCT 2.77%
AGGC 2.46%
CCCT 2.42%
AGAT 2.24%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis