Input data and parameters 

Input

Analysis date: Tue Oct 31 09:23:26 GMT 2023
BAM file: SRX7354364.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): 34,740,486 / 34,720,478
Number of aligned pairs (without duplicates): 34,701,275
Total number of alignments: 75,087,935
Number of secondary alignments: 5,626,971
Number of non-unique alignments: 9,207,791
Aligned to genes: 58,857,877
Ambiguous alignments: 257,335
No feature assigned: 6,244,729
Missing chromosome in annotation: 520,203
Not aligned: 1,446,782

Reads genomic origin

Exonic: 58,857,877 / 90.41%
Intronic: 3,616,236 / 5.55%
Intergenic: 2,628,493 / 4.04%
Intronic/intergenic overlapping exon: 2,732,252 / 4.2%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.26
5'-3' bias: 1.95

Junction analysis

Reads at junctions: 18,475,952
ACCT 5.14%
TCCT 4.6%
AGGT 4.44%
ATCT 4.27%
CCCT 3.27%
AGGA 3.19%
GCCT 3.17%
AGCT 2.4%
AGGC 2.27%
TTCT 2.11%
GTCT 1.76%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis