Input data and parameters
Input
Analysis date: | Tue Oct 31 10:04:17 GMT 2023 |
BAM file: | SRX7354351.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): | 40,163,752 / 40,122,610 |
Number of aligned pairs (without duplicates): | 40,116,751 |
Total number of alignments: | 84,958,960 |
Number of secondary alignments: | 4,672,598 |
Number of non-unique alignments: | 7,877,302 |
Aligned to genes: | 66,056,398 |
Ambiguous alignments: | 207,353 |
No feature assigned: | 10,555,179 |
Missing chromosome in annotation: | 262,728 |
Not aligned: | 8,409,014 |
Reads genomic origin
Exonic: | 66,056,398 / 86.22% |
Intronic: | 7,162,990 / 9.35% |
Intergenic: | 3,392,189 / 4.43% |
Intronic/intergenic overlapping exon: | 2,691,737 / 3.51% |
Transcript coverage profile
5' bias: | 0.28 |
3' bias: | 0.17 |
5'-3' bias: | 2.05 |
Junction analysis
Reads at junctions: | 19,948,601 |
ACCT | 5.43% |
AGGT | 4.66% |
ATCT | 3.67% |
AGGA | 3.58% |
TCCT | 3.36% |
GCCT | 3.15% |
AGCT | 2.72% |
AGGC | 2.39% |
AGAT | 2.34% |
CCCT | 2.28% |
TTCT | 2.2% |