Input data and parameters
Input
Analysis date: | Sun Oct 29 01:22:36 GMT 2023 |
BAM file: | SRX7354071.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): | 43,894,751 / 43,874,614 |
Number of aligned pairs (without duplicates): | 43,867,255 |
Total number of alignments: | 96,740,860 |
Number of secondary alignments: | 8,971,495 |
Number of non-unique alignments: | 13,305,514 |
Aligned to genes: | 74,123,370 |
Ambiguous alignments: | 322,227 |
No feature assigned: | 7,631,213 |
Missing chromosome in annotation: | 1,358,536 |
Not aligned: | 2,457,257 |
Reads genomic origin
Exonic: | 74,123,370 / 90.67% |
Intronic: | 4,404,924 / 5.39% |
Intergenic: | 3,226,289 / 3.95% |
Intronic/intergenic overlapping exon: | 3,787,784 / 4.63% |
Transcript coverage profile
5' bias: | 0.11 |
3' bias: | 0.13 |
5'-3' bias: | 2.24 |
Junction analysis
Reads at junctions: | 26,142,734 |
TCCT | 5.54% |
ACCT | 5.18% |
ATCT | 4.42% |
AGGT | 4.2% |
CCCT | 3.37% |
AGGA | 3.01% |
GCCT | 2.36% |
AGGC | 2.25% |
TTCT | 2.18% |
TCCC | 1.96% |
AGCT | 1.91% |