Input data and parameters 

Input

Analysis date: Mon Oct 30 23:05:41 GMT 2023
BAM file: SRX7354230.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): 44,796,353 / 44,753,547
Number of aligned pairs (without duplicates): 44,746,807
Total number of alignments: 94,583,027
Number of secondary alignments: 5,033,127
Number of non-unique alignments: 8,563,093
Aligned to genes: 76,301,632
Ambiguous alignments: 261,557
No feature assigned: 9,217,344
Missing chromosome in annotation: 239,401
Not aligned: 9,582,926

Reads genomic origin

Exonic: 76,301,632 / 89.22%
Intronic: 6,084,217 / 7.11%
Intergenic: 3,133,127 / 3.66%
Intronic/intergenic overlapping exon: 3,071,367 / 3.59%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.22
5'-3' bias: 1.77

Junction analysis

Reads at junctions: 27,960,186
ACCT 5.51%
AGGT 4.81%
ATCT 3.59%
AGGA 3.42%
TCCT 3.38%
GCCT 3.14%
AGCT 2.71%
AGGC 2.47%
CCCT 2.43%
AGAT 2.16%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis