Input data and parameters
Input
Analysis date: | Mon Oct 30 12:43:08 GMT 2023 |
BAM file: | SRX7354213.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): | 28,048,816 / 28,021,102 |
Number of aligned pairs (without duplicates): | 28,017,984 |
Total number of alignments: | 59,352,689 |
Number of secondary alignments: | 3,282,771 |
Number of non-unique alignments: | 5,465,685 |
Aligned to genes: | 47,217,192 |
Ambiguous alignments: | 147,918 |
No feature assigned: | 6,316,598 |
Missing chromosome in annotation: | 205,296 |
Not aligned: | 8,007,288 |
Reads genomic origin
Exonic: | 47,217,192 / 88.2% |
Intronic: | 4,011,286 / 7.49% |
Intergenic: | 2,305,312 / 4.31% |
Intronic/intergenic overlapping exon: | 1,813,484 / 3.39% |
Transcript coverage profile
5' bias: | 0.33 |
3' bias: | 0.16 |
5'-3' bias: | 2.22 |
Junction analysis
Reads at junctions: | 16,740,286 |
ACCT | 5.21% |
AGGT | 5.07% |
AGGA | 3.72% |
ATCT | 3.7% |
TCCT | 3.42% |
AGCT | 2.82% |
GCCT | 2.77% |
AGGC | 2.48% |
CCCT | 2.38% |
AGAT | 2.24% |
TTCT | 2.16% |