Input data and parameters 

Input

Analysis date: Sun Oct 29 03:11:15 GMT 2023
BAM file: SRX7354128.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): 46,032,500 / 45,962,552
Number of aligned pairs (without duplicates): 45,956,236
Total number of alignments: 97,964,144
Number of secondary alignments: 5,969,092
Number of non-unique alignments: 10,173,868
Aligned to genes: 76,203,919
Ambiguous alignments: 243,861
No feature assigned: 11,005,406
Missing chromosome in annotation: 337,090
Not aligned: 6,763,126

Reads genomic origin

Exonic: 76,203,919 / 87.38%
Intronic: 6,821,866 / 7.82%
Intergenic: 4,183,540 / 4.8%
Intronic/intergenic overlapping exon: 2,978,549 / 3.42%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.18
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 22,900,508
ACCT 5.45%
AGGT 4.57%
ATCT 3.59%
AGGA 3.53%
TCCT 3.3%
GCCT 3.28%
AGCT 2.72%
CCCT 2.38%
AGGC 2.34%
AGAT 2.27%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis