Input data and parameters
Input
Analysis date: | Mon Oct 30 20:26:21 GMT 2023 |
BAM file: | SRX7354243.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): | 48,630,098 / 48,581,987 |
Number of aligned pairs (without duplicates): | 48,570,598 |
Total number of alignments: | 103,895,805 |
Number of secondary alignments: | 6,683,720 |
Number of non-unique alignments: | 10,743,495 |
Aligned to genes: | 83,213,850 |
Ambiguous alignments: | 331,531 |
No feature assigned: | 9,000,876 |
Missing chromosome in annotation: | 606,053 |
Not aligned: | 11,984,909 |
Reads genomic origin
Exonic: | 83,213,850 / 90.24% |
Intronic: | 5,023,006 / 5.45% |
Intergenic: | 3,977,870 / 4.31% |
Intronic/intergenic overlapping exon: | 3,500,552 / 3.8% |
Transcript coverage profile
5' bias: | 0.15 |
3' bias: | 0.16 |
5'-3' bias: | 2.01 |
Junction analysis
Reads at junctions: | 29,500,473 |
ACCT | 5.08% |
TCCT | 4.83% |
AGGT | 4.55% |
ATCT | 4.45% |
CCCT | 3.33% |
AGGA | 3.24% |
GCCT | 2.47% |
TTCT | 2.25% |
AGGC | 2.16% |
AGCT | 2.15% |
AGAA | 1.97% |