Input data and parameters
Input
Analysis date: | Tue Oct 31 10:16:33 GMT 2023 |
BAM file: | SRX7354384.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): | 56,137,570 / 56,076,345 |
Number of aligned pairs (without duplicates): | 56,069,686 |
Total number of alignments: | 122,057,020 |
Number of secondary alignments: | 9,843,105 |
Number of non-unique alignments: | 16,731,113 |
Aligned to genes: | 94,862,845 |
Ambiguous alignments: | 299,716 |
No feature assigned: | 9,490,222 |
Missing chromosome in annotation: | 673,124 |
Not aligned: | 5,289,045 |
Reads genomic origin
Exonic: | 94,862,845 / 90.91% |
Intronic: | 4,011,818 / 3.84% |
Intergenic: | 5,478,404 / 5.25% |
Intronic/intergenic overlapping exon: | 3,548,376 / 3.4% |
Transcript coverage profile
5' bias: | 0.26 |
3' bias: | 0.2 |
5'-3' bias: | 1.92 |
Junction analysis
Reads at junctions: | 26,780,016 |
ACCT | 5.39% |
AGGT | 4.46% |
TCCT | 3.85% |
ATCT | 3.78% |
AGGA | 3.38% |
GCCT | 3.2% |
CCCT | 2.46% |
AGCT | 2.38% |
AGGC | 2.26% |
TTCT | 2.26% |
AGAT | 1.96% |