?
- Read pairs total
- Total number of reads, each read pair counts as one.
- Reads with known barcodes
- Number of reads with a known barcode
- Reads trusted
- Number of reads trusted because they come from a known and well populated barcode with at least 40 reads.
- Reads modified
- Number of reads with a modified barcode. Note that barcodes were changed only if the new barcode had at least 5 reads
- Reads written
- Total number of reads written. (Reads with unknown barcodes are discarded by default.)
- Barcoded reads written
- Total number of barcoded reads written. (Reads with unknown barcodes are discarded by default.)
- Read pairs per barcode
- Distribution of read pairs per known and unknown barcode, before and after error correction. Modified reads show the number of read pairs in the new barcode prior to error correction.
Fastq processing
fastq1.txt
| Read pairs total | 89,456,633 | |
| Reads with known barcode | 82,978,544 | 92.8% |
| Reads trusted | 73,914,231 | 82.6% |
| Reads modified | 2,313,902 | 2.6% |
| Reads written | 85,292,446 | 95.3% |
| Barcoded reads written | 85,292,446 | 95.3% |
?
- Read pairs total
- Total number of reads, each read pair counts as one.
- Reads with known barcodes
- Number of reads with a known barcode
- Reads trusted
- Number of reads trusted because they come from a known and well populated barcode with at least 40 reads.
- Reads modified
- Number of reads with a modified barcode. Note that barcodes were changed only if the new barcode had at least 5 reads
- Reads written
- Total number of reads written. (Reads with unknown barcodes are discarded by default.)
- Barcoded reads written
- Total number of barcoded reads written. (Reads with unknown barcodes are discarded by default.)
- Read pairs per barcode
- Distribution of read pairs per known and unknown barcode, before and after error correction. Modified reads show the number of read pairs in the new barcode prior to error correction.
Fastq processing
fastq3.txt
| Read pairs total | 102,418,628 | |
| Reads with known barcode | 94,980,309 | 92.7% |
| Reads trusted | 87,063,479 | 85.0% |
| Reads modified | 2,660,778 | 2.6% |
| Reads written | 97,641,087 | 95.3% |
| Barcoded reads written | 97,641,087 | 95.3% |
?
- Reads total
- Total number of reads, each read pair counts as two.
- Barcoded reads
- Reads with the BX tag
- Reads excluded
- Reads excluded because of flag, low mapping quality, etc.
- MQ<20
- Number of reads excluded because of low mapping quality.
- Anomalous pair
- Reads from a pair mapped to different chromosomes.
- Filtered
- Number of reads excluded because of BAM flags.
- Duplicates
- Number of reads marked as duplicate.
- Unmapped
- Number of unmapped reads.
- Mate unmapped
- Number of reads with unmapped mate from the read pair.
- Supplementary
- Number of supplementary reads.
- Coverage
- Good reads were filtered by flag (0xf0c) and mapping quality (≥20). The x axis range was set to show at least 99.0% of the data.
- Number of bases after soft-clipping
- Histogram of read-lengths after trimming soft-clipped bases. Includes all mapped reads.
- Unclipped reads
- Number of mapped reads without soft-clips
Sequencing
| Reads total | 740,882,919 | |
| Barcoded reads | 740,882,919 | 100.0% |
| Reads excluded | 261,503,006 | 35.3% |
| .. MQ<20 | 75,028,109 | 10.1% |
| .. anomalous pair | 15,443,099 | 2.1% |
| .. filtered | 186,474,897 | 25.2% |
| .. duplicates | 117,938,950 | 15.9% |
| .. unmapped | 19,901,841 | 2.7% |
| .. mate unmapped | 20,537,134 | 2.8% |
| .. supplementary | 46,474,085 | 6.3% |
| Unclipped reads | 330,852,254 | 45.9% |
?
- Insert size
- Insert size distribution, includes all mapped read pairs. The x axis range was set to show at least 98.0% of the data with insert sizes bigger than 0 bp.
- Number of bases against fragment length
- Total number of bases in fragments of given length (includes bases with zero coverage). The fragment size is calculated as D + D/(N-1), where N is the number of read pairs within the fragment and D is the distance between the first and the last pair. All read pairs must map to the same chromosome with the maximum gap of 100,000 bp. At least 5 read pairs per fragment are required.
- Sequences bases against fragment length
- Total number of sequence in fragments of given length.
- Number of fragments against fragment length
- Cumulative frequency of estimated DNA fragment size. The fragment length is calculated as above.
Input DNA
?
- Read pairs total
- Total number of reads, each read pair counts as one.
- Reads with known barcodes
- Number of reads with a known barcode
- Reads trusted
- Number of reads trusted because they come from a known and well populated barcode with at least 40 reads.
- Reads modified
- Number of reads with a modified barcode. Note that barcodes were changed only if the new barcode had at least 5 reads
- Reads written
- Total number of reads written. (Reads with unknown barcodes are discarded by default.)
- Barcoded reads written
- Total number of barcoded reads written. (Reads with unknown barcodes are discarded by default.)
- Read pairs per barcode
- Distribution of read pairs per known and unknown barcode, before and after error correction. Modified reads show the number of read pairs in the new barcode prior to error correction.
Fastq processing
fastq2.txt
| Read pairs total | 72,026,093 | |
| Reads with known barcode | 66,848,355 | 92.8% |
| Reads trusted | 55,731,824 | 77.4% |
| Reads modified | 1,845,703 | 2.6% |
| Reads written | 68,694,058 | 95.4% |
| Barcoded reads written | 68,694,058 | 95.4% |
?
- Read pairs total
- Total number of reads, each read pair counts as one.
- Reads with known barcodes
- Number of reads with a known barcode
- Reads trusted
- Number of reads trusted because they come from a known and well populated barcode with at least 40 reads.
- Reads modified
- Number of reads with a modified barcode. Note that barcodes were changed only if the new barcode had at least 5 reads
- Reads written
- Total number of reads written. (Reads with unknown barcodes are discarded by default.)
- Barcoded reads written
- Total number of barcoded reads written. (Reads with unknown barcodes are discarded by default.)
- Read pairs per barcode
- Distribution of read pairs per known and unknown barcode, before and after error correction. Modified reads show the number of read pairs in the new barcode prior to error correction.
Fastq processing
fastq4.txt
| Read pairs total | 100,263,542 | |
| Reads with known barcode | 92,990,456 | 92.7% |
| Reads trusted | 84,897,200 | 84.7% |
| Reads modified | 2,586,370 | 2.6% |
| Reads written | 95,576,826 | 95.3% |
| Barcoded reads written | 95,576,826 | 95.3% |
?
- Unique barcodes total
- Number of barcode sequences (the BX tag) found in the data.
- Good GEMs
- "GEM" stands for Gel Bead in Emulsion. In the sequencing data GEM corresponds to a set of reads with the same BX tag. Good GEMs are barcodes which were not excluded from reasons given below.
- Excluded barcodes
- Number of excluded barcodes. Barcodes can be excluded because their sequence is not present in the list of 4,792,320 known barcode sequences, because there are too few read pairs with the same barcode sequence (<2) or because there is no good fragment (all reads with the same barcode map to different chromosomes).
- Reads in good GEMs
- Number of good reads in good GEMs (but not necessarily in good fragments).
- Reads in good fragments
- Number of good reads in good fragments. At least 5 read pairs per fragment are required.
- Fragment size N50
- Shortest fragment at 50% of the total length: sort fragments by their size in ascending order, mark the center of the entire length and report the size of the fragment which happens to be in the middle.
- Fragment size N10x, N20x
- Longest fragment at 10x (20x) genome coverage: sort fragments by their size in descending order, mark the point where the distance from the beginning divided by the genome length is at least 10 (20) and report the size of the fragment which happens to be at that point. Note that the genome length is determined from the BAM header as the sum of all contigs (565,965,562 bp).
- Read pairs per barcode
- Read pair frequency in barcodes with this many read pairs per barcode. The x axis range was set to include 93.0% of the data.
- Read pairs per fragment
- Read pair frequency in fragments with this many read pairs per fragment. The x axis range was set to include 0% of the data.
- Fragment coverage
- Average depth within fragments. The x axis range was set to include 0% of the data.
GEMs
| Unique barcodes total | 1,693,058 | |
| Good GEMs | 1,207,872 | 71.3% |
| Excluded barcodes | 485,186 | 28.7% |
| .. fewer than 2 good read pairs | 419,793 | 24.8% |
| .. no good fragments | 65,393 | 3.9% |
| .. unlisted barcode sequence | 0 | 0.0% |
| Reads in good GEMs | 471,993,130 | 63.7% |
| Reads in good fragments | 456,540,982 | 61.6% |
| Fragment size N50 | 59,820 | |
| .. N10x | 200,600 | |
| .. N20x | 169,100 |
