Input data and parameters
Input
Analysis date: | Tue Oct 31 09:48:08 GMT 2023 |
BAM file: | SRX7354367.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): | 36,812,997 / 36,790,647 |
Number of aligned pairs (without duplicates): | 36,787,653 |
Total number of alignments: | 77,810,803 |
Number of secondary alignments: | 4,207,159 |
Number of non-unique alignments: | 7,156,647 |
Aligned to genes: | 62,278,552 |
Ambiguous alignments: | 191,211 |
No feature assigned: | 7,932,149 |
Missing chromosome in annotation: | 252,244 |
Not aligned: | 3,510,024 |
Reads genomic origin
Exonic: | 62,278,552 / 88.7% |
Intronic: | 4,993,491 / 7.11% |
Intergenic: | 2,938,658 / 4.19% |
Intronic/intergenic overlapping exon: | 2,293,994 / 3.27% |
Transcript coverage profile
5' bias: | 0.31 |
3' bias: | 0.16 |
5'-3' bias: | 2.12 |
Junction analysis
Reads at junctions: | 18,914,375 |
ACCT | 5.43% |
AGGT | 4.69% |
ATCT | 3.7% |
AGGA | 3.56% |
TCCT | 3.37% |
GCCT | 3.34% |
AGCT | 2.71% |
AGGC | 2.34% |
AGAT | 2.29% |
CCCT | 2.27% |
TTCT | 2.2% |