Input data and parameters
Input
Analysis date: | Mon Oct 30 11:13:56 GMT 2023 |
BAM file: | SRX7354210.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): | 44,890,175 / 44,872,580 |
Number of aligned pairs (without duplicates): | 44,865,272 |
Total number of alignments: | 97,973,167 |
Number of secondary alignments: | 8,210,412 |
Number of non-unique alignments: | 12,356,701 |
Aligned to genes: | 76,578,948 |
Ambiguous alignments: | 282,933 |
No feature assigned: | 7,697,755 |
Missing chromosome in annotation: | 1,056,830 |
Not aligned: | 3,036,901 |
Reads genomic origin
Exonic: | 76,578,948 / 90.87% |
Intronic: | 4,940,927 / 5.86% |
Intergenic: | 2,756,828 / 3.27% |
Intronic/intergenic overlapping exon: | 3,620,386 / 4.3% |
Transcript coverage profile
5' bias: | 0.15 |
3' bias: | 0.16 |
5'-3' bias: | 2.15 |
Junction analysis
Reads at junctions: | 31,604,985 |
ACCT | 5.28% |
TCCT | 4.57% |
AGGT | 4.48% |
ATCT | 4.35% |
AGGA | 3.02% |
CCCT | 2.7% |
GCCT | 2.45% |
AGGC | 2.23% |
AGCT | 2% |
TTCT | 1.94% |
AACT | 1.83% |