Input data and parameters
Input
Analysis date: | Mon Oct 30 11:19:59 GMT 2023 |
BAM file: | SRX7354180.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): | 31,556,184 / 31,538,928 |
Number of aligned pairs (without duplicates): | 31,535,627 |
Total number of alignments: | 67,075,290 |
Number of secondary alignments: | 3,980,178 |
Number of non-unique alignments: | 6,581,649 |
Aligned to genes: | 52,544,695 |
Ambiguous alignments: | 190,639 |
No feature assigned: | 7,484,759 |
Missing chromosome in annotation: | 273,548 |
Not aligned: | 2,198,286 |
Reads genomic origin
Exonic: | 52,544,695 / 87.53% |
Intronic: | 5,401,780 / 9% |
Intergenic: | 2,082,979 / 3.47% |
Intronic/intergenic overlapping exon: | 2,081,688 / 3.47% |
Transcript coverage profile
5' bias: | 0.48 |
3' bias: | 0.21 |
5'-3' bias: | 1.96 |
Junction analysis
Reads at junctions: | 18,351,268 |
ACCT | 5.35% |
AGGT | 4.73% |
AGGA | 3.64% |
ATCT | 3.47% |
TCCT | 3.34% |
GCCT | 3.29% |
AGCT | 2.82% |
CCCT | 2.45% |
AGGC | 2.42% |
AGAT | 2.33% |
TTCT | 2.11% |