Input data and parameters
Input
Analysis date: | Sun Oct 29 01:53:05 GMT 2023 |
BAM file: | SRX7354055.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): | 51,044,481 / 51,001,192 |
Number of aligned pairs (without duplicates): | 50,986,108 |
Total number of alignments: | 109,931,316 |
Number of secondary alignments: | 7,885,643 |
Number of non-unique alignments: | 12,852,376 |
Aligned to genes: | 84,936,466 |
Ambiguous alignments: | 330,641 |
No feature assigned: | 11,116,317 |
Missing chromosome in annotation: | 695,516 |
Not aligned: | 2,076,971 |
Reads genomic origin
Exonic: | 84,936,466 / 88.43% |
Intronic: | 7,779,510 / 8.1% |
Intergenic: | 3,336,807 / 3.47% |
Intronic/intergenic overlapping exon: | 3,956,451 / 4.12% |
Transcript coverage profile
5' bias: | 0.48 |
3' bias: | 0.25 |
5'-3' bias: | 1.74 |
Junction analysis
Reads at junctions: | 31,922,768 |
ACCT | 5.49% |
AGGT | 4.59% |
ATCT | 3.69% |
GCCT | 3.62% |
TCCT | 3.56% |
AGGA | 3.2% |
CCCT | 2.69% |
AGCT | 2.66% |
AGGC | 2.38% |
TTCT | 2.26% |
AGAT | 1.97% |