Input data and parameters
Input
Analysis date: | Tue Oct 31 15:22:27 GMT 2023 |
BAM file: | SRX7354388.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): | 35,521,193 / 35,498,986 |
Number of aligned pairs (without duplicates): | 35,495,677 |
Total number of alignments: | 76,513,013 |
Number of secondary alignments: | 5,492,834 |
Number of non-unique alignments: | 9,115,514 |
Aligned to genes: | 56,459,338 |
Ambiguous alignments: | 217,474 |
No feature assigned: | 10,263,156 |
Missing chromosome in annotation: | 457,531 |
Not aligned: | 2,656,229 |
Reads genomic origin
Exonic: | 56,459,338 / 84.62% |
Intronic: | 5,405,562 / 8.1% |
Intergenic: | 4,857,594 / 7.28% |
Intronic/intergenic overlapping exon: | 2,326,555 / 3.49% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.28 |
5'-3' bias: | 1.75 |
Junction analysis
Reads at junctions: | 22,751,411 |
ACCT | 5.42% |
AGGT | 4.55% |
TCCT | 3.9% |
ATCT | 3.59% |
GCCT | 3.57% |
AGGA | 3.23% |
CCCT | 2.66% |
AGCT | 2.6% |
AGGC | 2.44% |
TTCT | 2.18% |
AGAT | 2.01% |