Input data and parameters
Input
Analysis date: | Tue Oct 31 01:11:53 GMT 2023 |
BAM file: | SRX7354266.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): | 28,143,212 / 28,129,061 |
Number of aligned pairs (without duplicates): | 28,127,383 |
Total number of alignments: | 59,965,308 |
Number of secondary alignments: | 3,693,035 |
Number of non-unique alignments: | 6,163,320 |
Aligned to genes: | 46,711,974 |
Ambiguous alignments: | 157,367 |
No feature assigned: | 6,676,428 |
Missing chromosome in annotation: | 256,219 |
Not aligned: | 1,250,291 |
Reads genomic origin
Exonic: | 46,711,974 / 87.49% |
Intronic: | 4,314,540 / 8.08% |
Intergenic: | 2,361,888 / 4.42% |
Intronic/intergenic overlapping exon: | 1,784,953 / 3.34% |
Transcript coverage profile
5' bias: | 0.35 |
3' bias: | 0.2 |
5'-3' bias: | 2.04 |
Junction analysis
Reads at junctions: | 14,102,502 |
ACCT | 5.3% |
AGGT | 4.85% |
AGGA | 3.7% |
ATCT | 3.59% |
TCCT | 3.38% |
GCCT | 2.89% |
AGCT | 2.8% |
AGAT | 2.43% |
CCCT | 2.41% |
AGGC | 2.39% |
TTCT | 2.2% |