Input data and parameters
Input
Analysis date: | Sun Oct 29 13:03:00 GMT 2023 |
BAM file: | SRX7354193.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): | 48,675,559 / 48,658,801 |
Number of aligned pairs (without duplicates): | 48,655,482 |
Total number of alignments: | 103,498,641 |
Number of secondary alignments: | 6,164,281 |
Number of non-unique alignments: | 9,590,359 |
Aligned to genes: | 79,671,351 |
Ambiguous alignments: | 274,876 |
No feature assigned: | 13,183,519 |
Missing chromosome in annotation: | 778,536 |
Not aligned: | 1,720,638 |
Reads genomic origin
Exonic: | 79,671,351 / 85.8% |
Intronic: | 8,715,007 / 9.39% |
Intergenic: | 4,468,512 / 4.81% |
Intronic/intergenic overlapping exon: | 3,295,311 / 3.55% |
Transcript coverage profile
5' bias: | 0.43 |
3' bias: | 0.28 |
5'-3' bias: | 1.66 |
Junction analysis
Reads at junctions: | 29,165,070 |
ACCT | 4.95% |
AGGT | 4.58% |
ATCT | 3.69% |
TCCT | 3.53% |
AGGA | 3.37% |
GCCT | 3.36% |
AGCT | 2.95% |
CCCT | 2.66% |
AGGC | 2.36% |
TTCT | 2.15% |
AGAT | 2.04% |