SCRI_ROOT_RNAseq_MultiQC_HTS_STAR_Report_Jm3101_v1.0_Walnut_2.0
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2023-12-23, 14:57 based on data in:
/share/dandekarlab/Houston/SCRI_Root_RNAseq_work/01-HTS_Preproc/share/dandekarlab/Houston/SCRI_Root_RNAseq_work/05-STAR_alignment_2pass_combined_genomes
General Statistics
Showing 84/84 rows and 2/2 columns.| Sample Name | % Aligned | M Aligned |
|---|---|---|
| 29JM-11-1 | 76.3% | 2.5 |
| 29JM-11-1__STARpass1 | 76.3% | 2.5 |
| 29JM-11-2 | 67.6% | 0.8 |
| 29JM-11-2__STARpass1 | 67.5% | 0.8 |
| 29JM-11-3 | 77.7% | 3.0 |
| 29JM-11-3__STARpass1 | 77.8% | 3.0 |
| 29JM-11-4 | 81.0% | 5.2 |
| 29JM-11-4__STARpass1 | 81.0% | 5.3 |
| 29JM-11-5 | 81.3% | 6.2 |
| 29JM-11-5__STARpass1 | 81.4% | 6.2 |
| 29JM-11-6 | 86.5% | 7.5 |
| 29JM-11-6__STARpass1 | 86.7% | 7.5 |
| JMS-12-1 | 85.7% | 4.8 |
| JMS-12-1__STARpass1 | 85.8% | 4.9 |
| JMS-12-2 | 85.4% | 4.5 |
| JMS-12-2__STARpass1 | 85.6% | 4.5 |
| JMS-12-3 | 84.4% | 5.6 |
| JMS-12-3__STARpass1 | 84.5% | 5.6 |
| JMS-12-4 | 84.0% | 4.3 |
| JMS-12-4__STARpass1 | 84.1% | 4.3 |
| JMS-12-5 | 84.2% | 5.7 |
| JMS-12-5__STARpass1 | 84.4% | 5.7 |
| JMS-12-6 | 87.0% | 7.3 |
| JMS-12-6__STARpass1 | 87.1% | 7.3 |
| MS1-122-1 | 86.0% | 4.9 |
| MS1-122-1__STARpass1 | 86.1% | 4.9 |
| MS1-122-2 | 86.9% | 6.7 |
| MS1-122-2__STARpass1 | 87.0% | 6.7 |
| MS1-122-3 | 88.5% | 7.3 |
| MS1-122-3__STARpass1 | 88.6% | 7.3 |
| MS1-122-4 | 79.7% | 3.9 |
| MS1-122-4__STARpass1 | 79.7% | 3.9 |
| MS1-122-5 | 88.0% | 9.9 |
| MS1-122-5__STARpass1 | 88.1% | 9.9 |
| MS1-122-6 | 77.9% | 4.0 |
| MS1-122-6__STARpass1 | 77.9% | 4.0 |
| MS1-36-1 | 87.7% | 7.9 |
| MS1-36-1__STARpass1 | 88.0% | 7.9 |
| MS1-36-2 | 82.7% | 5.3 |
| MS1-36-2__STARpass1 | 83.0% | 5.4 |
| MS1-36-3 | 89.0% | 12.7 |
| MS1-36-3__STARpass1 | 89.2% | 12.7 |
| MS1-36-4 | 85.5% | 5.9 |
| MS1-36-4__STARpass1 | 85.8% | 5.9 |
| MS1-36-5 | 84.1% | 4.1 |
| MS1-36-5__STARpass1 | 84.4% | 4.1 |
| MS1-36-6 | 83.6% | 7.7 |
| MS1-36-6__STARpass1 | 83.8% | 7.8 |
| MS1-41-1 | 78.6% | 5.7 |
| MS1-41-1__STARpass1 | 78.7% | 5.7 |
| MS1-41-2 | 77.9% | 3.3 |
| MS1-41-2__STARpass1 | 78.0% | 3.3 |
| MS1-41-3 | 86.7% | 5.1 |
| MS1-41-3__STARpass1 | 86.8% | 5.1 |
| MS1-41-4 | 86.5% | 4.6 |
| MS1-41-4__STARpass1 | 86.7% | 4.6 |
| MS1-41-5 | 80.0% | 6.0 |
| MS1-41-5__STARpass1 | 80.1% | 6.0 |
| MS1-41-6 | 83.9% | 5.0 |
| MS1-41-6__STARpass1 | 84.1% | 5.0 |
| MS1-56-1 | 86.2% | 6.1 |
| MS1-56-1__STARpass1 | 86.5% | 6.1 |
| MS1-56-2 | 85.8% | 5.7 |
| MS1-56-2__STARpass1 | 86.1% | 5.7 |
| MS1-56-3 | 83.8% | 5.9 |
| MS1-56-3__STARpass1 | 84.0% | 5.9 |
| MS1-56-4 | 85.1% | 4.7 |
| MS1-56-4__STARpass1 | 85.3% | 4.7 |
| MS1-56-5 | 60.3% | 1.6 |
| MS1-56-5__STARpass1 | 60.1% | 1.6 |
| MS1-56-6 | 84.6% | 7.8 |
| MS1-56-6__STARpass1 | 84.9% | 7.8 |
| STJM-4-1 | 59.0% | 0.7 |
| STJM-4-1__STARpass1 | 59.0% | 0.7 |
| STJM-4-2 | 81.7% | 2.3 |
| STJM-4-2__STARpass1 | 82.0% | 2.3 |
| STJM-4-3 | 82.5% | 1.3 |
| STJM-4-3__STARpass1 | 82.8% | 1.4 |
| STJM-4-4 | 83.5% | 3.3 |
| STJM-4-4__STARpass1 | 83.7% | 3.3 |
| STJM-4-5 | 78.9% | 1.5 |
| STJM-4-5__STARpass1 | 79.1% | 1.5 |
| STJM-4-6 | 77.9% | 1.8 |
| STJM-4-6__STARpass1 | 77.9% | 1.8 |
STAR
STAR is an ultrafast universal RNA-seq aligner.
Alignment Scores
Gene Counts
Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.
HTStream
HTStream quality control and processing pipeline for High Throughput Sequencing data.
hts_Stats
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % PE | % R1 Q30 | % R2 Q30 | GC Content | N Content | Notes |
|---|---|---|---|---|---|---|
| 29JM-11-1 | 100.00% | 89.95% | 86.19% | 48.78% | 0.0000% | initial stats |
| 29JM-11-2 | 100.00% | 86.87% | 84.50% | 50.27% | 0.0000% | initial stats |
| 29JM-11-3 | 100.00% | 89.06% | 86.00% | 48.08% | 0.0000% | initial stats |
| 29JM-11-4 | 100.00% | 89.58% | 86.71% | 47.69% | 0.0000% | initial stats |
| 29JM-11-5 | 100.00% | 89.44% | 86.47% | 48.44% | 0.0000% | initial stats |
| 29JM-11-6 | 100.00% | 90.53% | 86.97% | 46.47% | 0.0000% | initial stats |
| JMS-12-1 | 100.00% | 90.14% | 86.46% | 46.18% | 0.0000% | initial stats |
| JMS-12-2 | 100.00% | 90.18% | 86.28% | 46.62% | 0.0000% | initial stats |
| JMS-12-3 | 100.00% | 90.60% | 86.83% | 46.27% | 0.0000% | initial stats |
| JMS-12-4 | 100.00% | 89.14% | 86.58% | 48.52% | 0.0000% | initial stats |
| JMS-12-5 | 100.00% | 90.15% | 86.38% | 46.36% | 0.0000% | initial stats |
| JMS-12-6 | 100.00% | 90.36% | 86.67% | 46.17% | 0.0000% | initial stats |
| MS1-122-1 | 100.00% | 89.93% | 84.79% | 45.76% | 0.0000% | initial stats |
| MS1-122-2 | 100.00% | 89.44% | 86.22% | 46.30% | 0.0000% | initial stats |
| MS1-122-3 | 100.00% | 89.34% | 83.76% | 46.41% | 0.0000% | initial stats |
| MS1-122-4 | 100.00% | 89.14% | 84.43% | 47.69% | 0.0000% | initial stats |
| MS1-122-5 | 100.00% | 89.41% | 85.95% | 46.18% | 0.0000% | initial stats |
| MS1-122-6 | 100.00% | 89.58% | 86.75% | 47.98% | 0.0000% | initial stats |
| MS1-36-1 | 100.00% | 89.76% | 85.56% | 46.47% | 0.0000% | initial stats |
| MS1-36-2 | 100.00% | 89.54% | 82.48% | 46.62% | 0.0000% | initial stats |
| MS1-36-3 | 100.00% | 90.71% | 85.49% | 45.79% | 0.0000% | initial stats |
| MS1-36-4 | 100.00% | 90.80% | 87.34% | 46.18% | 0.0000% | initial stats |
| MS1-36-5 | 100.00% | 88.71% | 83.98% | 47.56% | 0.0000% | initial stats |
| MS1-36-6 | 100.00% | 90.71% | 86.18% | 47.12% | 0.0000% | initial stats |
| MS1-41-1 | 100.00% | 89.81% | 86.50% | 46.46% | 0.0000% | initial stats |
| MS1-41-2 | 100.00% | 88.67% | 85.74% | 49.03% | 0.0000% | initial stats |
| MS1-41-3 | 100.00% | 90.09% | 85.91% | 46.46% | 0.0000% | initial stats |
| MS1-41-4 | 100.00% | 89.72% | 85.65% | 46.91% | 0.0000% | initial stats |
| MS1-41-5 | 100.00% | 89.73% | 86.31% | 49.19% | 0.0000% | initial stats |
| MS1-41-6 | 100.00% | 89.41% | 85.96% | 47.14% | 0.0000% | initial stats |
| MS1-56-1 | 100.00% | 89.40% | 86.18% | 46.52% | 0.0000% | initial stats |
| MS1-56-2 | 100.00% | 89.40% | 85.97% | 47.35% | 0.0000% | initial stats |
| MS1-56-3 | 100.00% | 89.78% | 86.63% | 47.04% | 0.0000% | initial stats |
| MS1-56-4 | 100.00% | 90.23% | 87.04% | 47.05% | 0.0000% | initial stats |
| MS1-56-5 | 100.00% | 89.01% | 86.58% | 51.90% | 0.0000% | initial stats |
| MS1-56-6 | 100.00% | 90.49% | 87.13% | 47.99% | 0.0000% | initial stats |
| STJM-4-1 | 100.00% | 86.14% | 85.65% | 52.02% | 0.0000% | initial stats |
| STJM-4-2 | 100.00% | 88.29% | 86.19% | 47.83% | 0.0000% | initial stats |
| STJM-4-3 | 100.00% | 88.24% | 85.31% | 46.71% | 0.0000% | initial stats |
| STJM-4-4 | 100.00% | 89.92% | 86.18% | 47.84% | 0.0000% | initial stats |
| STJM-4-5 | 100.00% | 87.84% | 85.25% | 48.26% | 0.0000% | initial stats |
| STJM-4-6 | 100.00% | 89.11% | 85.65% | 48.27% | 0.0000% | initial stats |
Read Lengths: Paired End
Distribution of read lengths for each sample.
Notice: Each sample has a uniform read length distribution.
Showing 42/42 rows and 2/2 columns.
| Sample Name | R1 Read Lengths | R2 Read Lengths |
|---|---|---|
| 29JM-11-1 | 151 | 151 |
| 29JM-11-2 | 151 | 151 |
| 29JM-11-3 | 151 | 151 |
| 29JM-11-4 | 151 | 151 |
| 29JM-11-5 | 151 | 151 |
| 29JM-11-6 | 151 | 151 |
| JMS-12-1 | 151 | 151 |
| JMS-12-2 | 151 | 151 |
| JMS-12-3 | 151 | 151 |
| JMS-12-4 | 151 | 151 |
| JMS-12-5 | 151 | 151 |
| JMS-12-6 | 151 | 151 |
| MS1-122-1 | 151 | 151 |
| MS1-122-2 | 151 | 151 |
| MS1-122-3 | 151 | 151 |
| MS1-122-4 | 151 | 151 |
| MS1-122-5 | 151 | 151 |
| MS1-122-6 | 151 | 151 |
| MS1-36-1 | 151 | 151 |
| MS1-36-2 | 151 | 151 |
| MS1-36-3 | 151 | 151 |
| MS1-36-4 | 151 | 151 |
| MS1-36-5 | 151 | 151 |
| MS1-36-6 | 151 | 151 |
| MS1-41-1 | 151 | 151 |
| MS1-41-2 | 151 | 151 |
| MS1-41-3 | 151 | 151 |
| MS1-41-4 | 151 | 151 |
| MS1-41-5 | 151 | 151 |
| MS1-41-6 | 151 | 151 |
| MS1-56-1 | 151 | 151 |
| MS1-56-2 | 151 | 151 |
| MS1-56-3 | 151 | 151 |
| MS1-56-4 | 151 | 151 |
| MS1-56-5 | 151 | 151 |
| MS1-56-6 | 151 | 151 |
| STJM-4-1 | 151 | 151 |
| STJM-4-2 | 151 | 151 |
| STJM-4-3 | 151 | 151 |
| STJM-4-4 | 151 | 151 |
| STJM-4-5 | 151 | 151 |
| STJM-4-6 | 151 | 151 |
Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.
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Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
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hts_SeqScreener
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
| Sample Name | PE hits | % PE Hits | Notes |
|---|---|---|---|
| 29JM-11-1 | 1 | 0.0000% | screen phix |
| 29JM-11-2 | 0 | 0.0000% | screen phix |
| 29JM-11-3 | 0 | 0.0000% | screen phix |
| 29JM-11-4 | 0 | 0.0000% | screen phix |
| 29JM-11-5 | 0 | 0.0000% | screen phix |
| 29JM-11-6 | 0 | 0.0000% | screen phix |
| JMS-12-1 | 0 | 0.0000% | screen phix |
| JMS-12-2 | 2 | 0.0000% | screen phix |
| JMS-12-3 | 0 | 0.0000% | screen phix |
| JMS-12-4 | 1 | 0.0000% | screen phix |
| JMS-12-5 | 3 | 0.0000% | screen phix |
| JMS-12-6 | 1 | 0.0000% | screen phix |
| MS1-122-1 | 0 | 0.0000% | screen phix |
| MS1-122-2 | 0 | 0.0000% | screen phix |
| MS1-122-3 | 0 | 0.0000% | screen phix |
| MS1-122-4 | 0 | 0.0000% | screen phix |
| MS1-122-5 | 0 | 0.0000% | screen phix |
| MS1-122-6 | 2 | 0.0000% | screen phix |
| MS1-36-1 | 0 | 0.0000% | screen phix |
| MS1-36-2 | 0 | 0.0000% | screen phix |
| MS1-36-3 | 0 | 0.0000% | screen phix |
| MS1-36-4 | 1 | 0.0000% | screen phix |
| MS1-36-5 | 0 | 0.0000% | screen phix |
| MS1-36-6 | 0 | 0.0000% | screen phix |
| MS1-41-1 | 0 | 0.0000% | screen phix |
| MS1-41-2 | 0 | 0.0000% | screen phix |
| MS1-41-3 | 0 | 0.0000% | screen phix |
| MS1-41-4 | 0 | 0.0000% | screen phix |
| MS1-41-5 | 0 | 0.0000% | screen phix |
| MS1-41-6 | 1 | 0.0000% | screen phix |
| MS1-56-1 | 0 | 0.0000% | screen phix |
| MS1-56-2 | 0 | 0.0000% | screen phix |
| MS1-56-3 | 0 | 0.0000% | screen phix |
| MS1-56-4 | 2 | 0.0000% | screen phix |
| MS1-56-5 | 1 | 0.0000% | screen phix |
| MS1-56-6 | 1 | 0.0000% | screen phix |
| STJM-4-1 | 0 | 0.0000% | screen phix |
| STJM-4-2 | 1 | 0.0000% | screen phix |
| STJM-4-3 | 0 | 0.0000% | screen phix |
| STJM-4-4 | 3 | 0.0000% | screen phix |
| STJM-4-5 | 0 | 0.0000% | screen phix |
| STJM-4-6 | 0 | 0.0000% | screen phix |
hts_SeqScreener 2
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
| Sample Name | PE hits | % PE Hits | Notes |
|---|---|---|---|
| 29JM-11-1 | 3093995 | 21.6919% | count the number of rRNA reads |
| 29JM-11-2 | 4061581 | 41.7823% | count the number of rRNA reads |
| 29JM-11-3 | 2926056 | 24.6395% | count the number of rRNA reads |
| 29JM-11-4 | 3746781 | 20.0501% | count the number of rRNA reads |
| 29JM-11-5 | 4634312 | 27.0060% | count the number of rRNA reads |
| 29JM-11-6 | 239295 | 1.1400% | count the number of rRNA reads |
| JMS-12-1 | 172648 | 1.2984% | count the number of rRNA reads |
| JMS-12-2 | 547911 | 4.9555% | count the number of rRNA reads |
| JMS-12-3 | 808672 | 5.1465% | count the number of rRNA reads |
| JMS-12-4 | 3004810 | 27.8810% | count the number of rRNA reads |
| JMS-12-5 | 692571 | 4.4940% | count the number of rRNA reads |
| JMS-12-6 | 230864 | 1.6761% | count the number of rRNA reads |
| MS1-122-1 | 138010 | 1.2019% | count the number of rRNA reads |
| MS1-122-2 | 548745 | 3.4746% | count the number of rRNA reads |
| MS1-122-3 | 505136 | 3.1594% | count the number of rRNA reads |
| MS1-122-4 | 2801765 | 15.7665% | count the number of rRNA reads |
| MS1-122-5 | 719335 | 3.8210% | count the number of rRNA reads |
| MS1-122-6 | 4411886 | 22.8508% | count the number of rRNA reads |
| MS1-36-1 | 642047 | 3.0498% | count the number of rRNA reads |
| MS1-36-2 | 1477544 | 6.3310% | count the number of rRNA reads |
| MS1-36-3 | 328659 | 1.5200% | count the number of rRNA reads |
| MS1-36-4 | 339714 | 2.6586% | count the number of rRNA reads |
| MS1-36-5 | 1614528 | 11.6100% | count the number of rRNA reads |
| MS1-36-6 | 2975559 | 11.1945% | count the number of rRNA reads |
| MS1-41-1 | 2602501 | 13.4520% | count the number of rRNA reads |
| MS1-41-2 | 3546070 | 27.8019% | count the number of rRNA reads |
| MS1-41-3 | 314666 | 2.9254% | count the number of rRNA reads |
| MS1-41-4 | 395811 | 4.0205% | count the number of rRNA reads |
| MS1-41-5 | 5689857 | 24.8027% | count the number of rRNA reads |
| MS1-41-6 | 1580991 | 10.0976% | count the number of rRNA reads |
| MS1-56-1 | 474936 | 2.6893% | count the number of rRNA reads |
| MS1-56-2 | 1401384 | 8.1975% | count the number of rRNA reads |
| MS1-56-3 | 953551 | 5.8386% | count the number of rRNA reads |
| MS1-56-4 | 866827 | 7.1640% | count the number of rRNA reads |
| MS1-56-5 | 8185566 | 62.0490% | count the number of rRNA reads |
| MS1-56-6 | 3294702 | 13.4853% | count the number of rRNA reads |
| STJM-4-1 | 6421285 | 61.4649% | count the number of rRNA reads |
| STJM-4-2 | 672639 | 4.2700% | count the number of rRNA reads |
| STJM-4-3 | 190321 | 1.9589% | count the number of rRNA reads |
| STJM-4-4 | 1009984 | 7.9049% | count the number of rRNA reads |
| STJM-4-5 | 1374979 | 10.2073% | count the number of rRNA reads |
| STJM-4-6 | 1763251 | 16.5958% | count the number of rRNA reads |
hts_SuperDeduper
A reference free duplicate read removal tool.
| Sample Name | % Duplicates | % Ignored | Notes |
|---|---|---|---|
| 29JM-11-1 | 76.94% | 0.00% | remove PCR duplicates |
| 29JM-11-2 | 88.32% | 0.00% | remove PCR duplicates |
| 29JM-11-3 | 68.00% | 0.00% | remove PCR duplicates |
| 29JM-11-4 | 65.30% | 0.00% | remove PCR duplicates |
| 29JM-11-5 | 55.68% | 0.00% | remove PCR duplicates |
| 29JM-11-6 | 58.92% | 0.00% | remove PCR duplicates |
| JMS-12-1 | 57.40% | 0.00% | remove PCR duplicates |
| JMS-12-2 | 52.06% | 0.00% | remove PCR duplicates |
| JMS-12-3 | 57.80% | 0.00% | remove PCR duplicates |
| JMS-12-4 | 52.85% | 0.00% | remove PCR duplicates |
| JMS-12-5 | 56.14% | 0.00% | remove PCR duplicates |
| JMS-12-6 | 39.00% | 0.00% | remove PCR duplicates |
| MS1-122-1 | 50.35% | 0.00% | remove PCR duplicates |
| MS1-122-2 | 50.99% | 0.00% | remove PCR duplicates |
| MS1-122-3 | 48.44% | 0.00% | remove PCR duplicates |
| MS1-122-4 | 72.74% | 0.00% | remove PCR duplicates |
| MS1-122-5 | 40.25% | 0.00% | remove PCR duplicates |
| MS1-122-6 | 73.14% | 0.00% | remove PCR duplicates |
| MS1-36-1 | 57.28% | 0.00% | remove PCR duplicates |
| MS1-36-2 | 72.32% | 0.00% | remove PCR duplicates |
| MS1-36-3 | 34.10% | 0.00% | remove PCR duplicates |
| MS1-36-4 | 46.29% | 0.00% | remove PCR duplicates |
| MS1-36-5 | 64.75% | 0.00% | remove PCR duplicates |
| MS1-36-6 | 65.12% | 0.00% | remove PCR duplicates |
| MS1-41-1 | 62.24% | 0.00% | remove PCR duplicates |
| MS1-41-2 | 66.74% | 0.00% | remove PCR duplicates |
| MS1-41-3 | 45.55% | 0.00% | remove PCR duplicates |
| MS1-41-4 | 45.78% | 0.00% | remove PCR duplicates |
| MS1-41-5 | 67.23% | 0.00% | remove PCR duplicates |
| MS1-41-6 | 62.07% | 0.00% | remove PCR duplicates |
| MS1-56-1 | 59.95% | 0.00% | remove PCR duplicates |
| MS1-56-2 | 61.34% | 0.00% | remove PCR duplicates |
| MS1-56-3 | 57.05% | 0.00% | remove PCR duplicates |
| MS1-56-4 | 54.76% | 0.00% | remove PCR duplicates |
| MS1-56-5 | 79.39% | 0.00% | remove PCR duplicates |
| MS1-56-6 | 62.21% | 0.00% | remove PCR duplicates |
| STJM-4-1 | 89.31% | 0.00% | remove PCR duplicates |
| STJM-4-2 | 81.81% | 0.00% | remove PCR duplicates |
| STJM-4-3 | 83.16% | 0.00% | remove PCR duplicates |
| STJM-4-4 | 69.37% | 0.00% | remove PCR duplicates |
| STJM-4-5 | 85.72% | 0.00% | remove PCR duplicates |
| STJM-4-6 | 78.60% | 0.00% | remove PCR duplicates |
SuperDeduper: Duplicate Saturation
Plots the number of duplicates against the number of unique reads per sample.
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hts_AdapterTrimmer
Trims adapters which are sequenced when the fragment insert length is shorter than the read length.
| Sample Name | % Bp Lost | % Adapters | Avg. Bps Trimmed | Notes |
|---|---|---|---|---|
| 29JM-11-1 | 4.99% | 44.71% | 33.67 | trim adapters |
| 29JM-11-2 | 1.92% | 17.47% | 33.10 | trim adapters |
| 29JM-11-3 | 5.35% | 46.86% | 34.47 | trim adapters |
| 29JM-11-4 | 4.87% | 43.24% | 34.02 | trim adapters |
| 29JM-11-5 | 4.89% | 44.18% | 33.41 | trim adapters |
| 29JM-11-6 | 4.57% | 42.20% | 32.69 | trim adapters |
| JMS-12-1 | 5.31% | 47.35% | 33.85 | trim adapters |
| JMS-12-2 | 3.83% | 37.89% | 30.50 | trim adapters |
| JMS-12-3 | 5.58% | 51.62% | 32.65 | trim adapters |
| JMS-12-4 | 6.82% | 60.13% | 34.28 | trim adapters |
| JMS-12-5 | 5.65% | 52.14% | 32.74 | trim adapters |
| JMS-12-6 | 3.85% | 34.85% | 33.35 | trim adapters |
| MS1-122-1 | 5.35% | 47.52% | 34.01 | trim adapters |
| MS1-122-2 | 3.95% | 35.16% | 33.94 | trim adapters |
| MS1-122-3 | 3.01% | 27.39% | 33.14 | trim adapters |
| MS1-122-4 | 3.73% | 33.25% | 33.85 | trim adapters |
| MS1-122-5 | 3.43% | 30.58% | 33.88 | trim adapters |
| MS1-122-6 | 4.29% | 39.96% | 32.39 | trim adapters |
| MS1-36-1 | 3.07% | 30.08% | 30.82 | trim adapters |
| MS1-36-2 | 4.01% | 37.71% | 32.15 | trim adapters |
| MS1-36-3 | 4.08% | 37.45% | 32.94 | trim adapters |
| MS1-36-4 | 6.61% | 59.95% | 33.32 | trim adapters |
| MS1-36-5 | 2.92% | 27.10% | 32.53 | trim adapters |
| MS1-36-6 | 3.61% | 31.80% | 34.29 | trim adapters |
| MS1-41-1 | 5.61% | 49.56% | 34.20 | trim adapters |
| MS1-41-2 | 4.68% | 41.18% | 34.29 | trim adapters |
| MS1-41-3 | 4.39% | 40.28% | 32.90 | trim adapters |
| MS1-41-4 | 4.24% | 37.93% | 33.72 | trim adapters |
| MS1-41-5 | 4.09% | 36.70% | 33.69 | trim adapters |
| MS1-41-6 | 4.01% | 35.78% | 33.82 | trim adapters |
| MS1-56-1 | 3.16% | 30.22% | 31.62 | trim adapters |
| MS1-56-2 | 3.65% | 34.03% | 32.41 | trim adapters |
| MS1-56-3 | 4.63% | 42.25% | 33.10 | trim adapters |
| MS1-56-4 | 5.11% | 48.52% | 31.79 | trim adapters |
| MS1-56-5 | 4.00% | 36.64% | 33.01 | trim adapters |
| MS1-56-6 | 4.09% | 38.09% | 32.40 | trim adapters |
| STJM-4-1 | 2.32% | 21.79% | 32.22 | trim adapters |
| STJM-4-2 | 3.28% | 29.96% | 33.09 | trim adapters |
| STJM-4-3 | 2.57% | 24.14% | 32.12 | trim adapters |
| STJM-4-4 | 3.58% | 32.58% | 33.16 | trim adapters |
| STJM-4-5 | 3.25% | 30.31% | 32.40 | trim adapters |
| STJM-4-6 | 4.05% | 37.18% | 32.86 | trim adapters |
AdapterTrimmer: Trimmed Basepairs Composition
Composition of basepairs trimmed from the ends of paired end and single end reads.
hts_PolyATTrim
Attempts to trim poly-A and poly-T sequences from the end of reads.
| Sample Name | Total Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | Notes |
|---|---|---|---|---|
| 29JM-11-1 | 25189 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-2 | 11035 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-3 | 40364 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-4 | 76357 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-5 | 85171 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-6 | 100950 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-1 | 67682 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-2 | 61972 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-3 | 84637 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-4 | 65092 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-5 | 88380 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-6 | 106881 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-1 | 56933 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-2 | 79320 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-3 | 90020 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-4 | 42163 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-5 | 120556 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-6 | 52842 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-1 | 112492 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-2 | 79717 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-3 | 191250 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-4 | 81856 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-5 | 46937 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-6 | 81022 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-1 | 64490 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-2 | 34000 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-3 | 57790 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-4 | 54140 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-5 | 63013 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-6 | 57626 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-1 | 90586 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-2 | 78266 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-3 | 85127 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-4 | 58196 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-5 | 20103 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-6 | 99142 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-1 | 7725 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-2 | 29193 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-3 | 20113 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-4 | 41296 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-5 | 18833 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-6 | 22744 | 0.00% | 100.00% | remove polyAT tails |
hts_NTrimmer
Trims reads to the longest subsequence that contains no N's.
| Sample Name | Total Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | % Discarded | Notes |
|---|---|---|---|---|---|
| 29JM-11-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-4 | -1 | -0.00% | 100.00% | 0.00% | remove any remaining N characters |
| MS1-41-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
NTrimmer: Trimmed Basepairs Composition
Plots the number of N bases trimmed from ends of paired end and single end reads.
hts_QWindowTrim
Uses a sliding window approach to remove the low quality ends of reads.
| Sample Name | % Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | Avg. Bps Trimmed | Notes |
|---|---|---|---|---|---|
| 29JM-11-1 | 0.48% | 18.72% | 81.28% | 1.38 | quality trim the ends of reads |
| 29JM-11-2 | 0.69% | 18.70% | 81.30% | 2.03 | quality trim the ends of reads |
| 29JM-11-3 | 0.33% | 23.14% | 76.86% | 0.94 | quality trim the ends of reads |
| 29JM-11-4 | 0.22% | 31.36% | 68.64% | 0.63 | quality trim the ends of reads |
| 29JM-11-5 | 0.24% | 28.38% | 71.62% | 0.69 | quality trim the ends of reads |
| 29JM-11-6 | 0.23% | 30.91% | 69.09% | 0.65 | quality trim the ends of reads |
| JMS-12-1 | 0.25% | 26.21% | 73.79% | 0.72 | quality trim the ends of reads |
| JMS-12-2 | 0.27% | 26.39% | 73.61% | 0.78 | quality trim the ends of reads |
| JMS-12-3 | 0.24% | 28.49% | 71.51% | 0.70 | quality trim the ends of reads |
| JMS-12-4 | 0.24% | 27.58% | 72.42% | 0.69 | quality trim the ends of reads |
| JMS-12-5 | 0.25% | 27.58% | 72.42% | 0.72 | quality trim the ends of reads |
| JMS-12-6 | 0.20% | 34.01% | 65.99% | 0.57 | quality trim the ends of reads |
| MS1-122-1 | 0.33% | 21.48% | 78.52% | 0.94 | quality trim the ends of reads |
| MS1-122-2 | 0.20% | 32.66% | 67.34% | 0.58 | quality trim the ends of reads |
| MS1-122-3 | 0.20% | 31.14% | 68.86% | 0.60 | quality trim the ends of reads |
| MS1-122-4 | 0.28% | 27.82% | 72.18% | 0.83 | quality trim the ends of reads |
| MS1-122-5 | 0.19% | 34.34% | 65.66% | 0.54 | quality trim the ends of reads |
| MS1-122-6 | 0.28% | 30.06% | 69.94% | 0.81 | quality trim the ends of reads |
| MS1-36-1 | 0.24% | 30.07% | 69.93% | 0.70 | quality trim the ends of reads |
| MS1-36-2 | 0.32% | 28.01% | 71.99% | 0.93 | quality trim the ends of reads |
| MS1-36-3 | 0.22% | 31.88% | 68.12% | 0.63 | quality trim the ends of reads |
| MS1-36-4 | 0.24% | 25.23% | 74.77% | 0.69 | quality trim the ends of reads |
| MS1-36-5 | 0.25% | 31.41% | 68.59% | 0.73 | quality trim the ends of reads |
| MS1-36-6 | 0.29% | 26.46% | 73.54% | 0.85 | quality trim the ends of reads |
| MS1-41-1 | 0.25% | 31.08% | 68.92% | 0.72 | quality trim the ends of reads |
| MS1-41-2 | 0.32% | 24.78% | 75.22% | 0.93 | quality trim the ends of reads |
| MS1-41-3 | 0.27% | 25.50% | 74.50% | 0.79 | quality trim the ends of reads |
| MS1-41-4 | 0.25% | 26.88% | 73.12% | 0.72 | quality trim the ends of reads |
| MS1-41-5 | 0.27% | 28.21% | 71.79% | 0.79 | quality trim the ends of reads |
| MS1-41-6 | 0.27% | 27.84% | 72.16% | 0.79 | quality trim the ends of reads |
| MS1-56-1 | 0.27% | 30.69% | 69.31% | 0.78 | quality trim the ends of reads |
| MS1-56-2 | 0.25% | 32.78% | 67.22% | 0.71 | quality trim the ends of reads |
| MS1-56-3 | 0.23% | 30.84% | 69.16% | 0.67 | quality trim the ends of reads |
| MS1-56-4 | 0.24% | 27.01% | 72.99% | 0.68 | quality trim the ends of reads |
| MS1-56-5 | 0.38% | 27.69% | 72.31% | 1.11 | quality trim the ends of reads |
| MS1-56-6 | 0.25% | 31.93% | 68.07% | 0.74 | quality trim the ends of reads |
| STJM-4-1 | 0.65% | 22.38% | 77.62% | 1.91 | quality trim the ends of reads |
| STJM-4-2 | 0.32% | 29.61% | 70.39% | 0.93 | quality trim the ends of reads |
| STJM-4-3 | 0.53% | 18.56% | 81.44% | 1.55 | quality trim the ends of reads |
| STJM-4-4 | 0.26% | 27.98% | 72.02% | 0.77 | quality trim the ends of reads |
| STJM-4-5 | 0.52% | 21.66% | 78.34% | 1.53 | quality trim the ends of reads |
| STJM-4-6 | 0.48% | 19.27% | 80.73% | 1.38 | quality trim the ends of reads |
QWindowTrim: Trimmed Basepairs Composition
Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.
hts_LengthFilter
Discards reads below a minimum length threshold.
| Sample Name | % PE Lost | Notes |
|---|---|---|
| 29JM-11-1 | 0.13% | remove reads < 50bp |
| 29JM-11-2 | 0.26% | remove reads < 50bp |
| 29JM-11-3 | 0.09% | remove reads < 50bp |
| 29JM-11-4 | 0.04% | remove reads < 50bp |
| 29JM-11-5 | 0.06% | remove reads < 50bp |
| 29JM-11-6 | 0.04% | remove reads < 50bp |
| JMS-12-1 | 0.06% | remove reads < 50bp |
| JMS-12-2 | 0.07% | remove reads < 50bp |
| JMS-12-3 | 0.05% | remove reads < 50bp |
| JMS-12-4 | 0.05% | remove reads < 50bp |
| JMS-12-5 | 0.06% | remove reads < 50bp |
| JMS-12-6 | 0.03% | remove reads < 50bp |
| MS1-122-1 | 0.12% | remove reads < 50bp |
| MS1-122-2 | 0.04% | remove reads < 50bp |
| MS1-122-3 | 0.04% | remove reads < 50bp |
| MS1-122-4 | 0.05% | remove reads < 50bp |
| MS1-122-5 | 0.03% | remove reads < 50bp |
| MS1-122-6 | 0.05% | remove reads < 50bp |
| MS1-36-1 | 0.05% | remove reads < 50bp |
| MS1-36-2 | 0.06% | remove reads < 50bp |
| MS1-36-3 | 0.04% | remove reads < 50bp |
| MS1-36-4 | 0.07% | remove reads < 50bp |
| MS1-36-5 | 0.05% | remove reads < 50bp |
| MS1-36-6 | 0.06% | remove reads < 50bp |
| MS1-41-1 | 0.05% | remove reads < 50bp |
| MS1-41-2 | 0.08% | remove reads < 50bp |
| MS1-41-3 | 0.07% | remove reads < 50bp |
| MS1-41-4 | 0.07% | remove reads < 50bp |
| MS1-41-5 | 0.05% | remove reads < 50bp |
| MS1-41-6 | 0.06% | remove reads < 50bp |
| MS1-56-1 | 0.05% | remove reads < 50bp |
| MS1-56-2 | 0.04% | remove reads < 50bp |
| MS1-56-3 | 0.05% | remove reads < 50bp |
| MS1-56-4 | 0.06% | remove reads < 50bp |
| MS1-56-5 | 0.06% | remove reads < 50bp |
| MS1-56-6 | 0.04% | remove reads < 50bp |
| STJM-4-1 | 0.15% | remove reads < 50bp |
| STJM-4-2 | 0.06% | remove reads < 50bp |
| STJM-4-3 | 0.18% | remove reads < 50bp |
| STJM-4-4 | 0.05% | remove reads < 50bp |
| STJM-4-5 | 0.17% | remove reads < 50bp |
| STJM-4-6 | 0.14% | remove reads < 50bp |
hts_Stats 2
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % PE | % R1 Q30 | % R2 Q30 | GC Content | N Content | Notes |
|---|---|---|---|---|---|---|
| 29JM-11-1 | 100.00% | 93.68% | 88.40% | 47.82% | 0.0000% | final stats |
| 29JM-11-2 | 100.00% | 90.32% | 84.23% | 48.40% | 0.0000% | final stats |
| 29JM-11-3 | 100.00% | 94.22% | 90.62% | 46.45% | 0.0000% | final stats |
| 29JM-11-4 | 100.00% | 94.65% | 91.86% | 46.20% | 0.0000% | final stats |
| 29JM-11-5 | 100.00% | 94.73% | 91.86% | 46.31% | 0.0000% | final stats |
| 29JM-11-6 | 100.00% | 95.01% | 91.84% | 46.48% | 0.0000% | final stats |
| JMS-12-1 | 100.00% | 94.99% | 91.86% | 45.83% | 0.0000% | final stats |
| JMS-12-2 | 100.00% | 94.83% | 91.57% | 46.36% | 0.0000% | final stats |
| JMS-12-3 | 100.00% | 95.16% | 91.95% | 46.01% | 0.0000% | final stats |
| JMS-12-4 | 100.00% | 95.35% | 92.19% | 45.74% | 0.0000% | final stats |
| JMS-12-5 | 100.00% | 95.06% | 92.00% | 45.77% | 0.0000% | final stats |
| JMS-12-6 | 100.00% | 94.68% | 91.91% | 45.85% | 0.0000% | final stats |
| MS1-122-1 | 100.00% | 94.77% | 90.76% | 45.34% | 0.0000% | final stats |
| MS1-122-2 | 100.00% | 94.45% | 91.89% | 45.83% | 0.0000% | final stats |
| MS1-122-3 | 100.00% | 94.22% | 90.27% | 45.95% | 0.0000% | final stats |
| MS1-122-4 | 100.00% | 93.46% | 89.40% | 47.12% | 0.0000% | final stats |
| MS1-122-5 | 100.00% | 94.19% | 91.57% | 45.65% | 0.0000% | final stats |
| MS1-122-6 | 100.00% | 94.13% | 90.67% | 46.96% | 0.0000% | final stats |
| MS1-36-1 | 100.00% | 94.38% | 90.77% | 46.02% | 0.0000% | final stats |
| MS1-36-2 | 100.00% | 93.73% | 88.40% | 46.49% | 0.0000% | final stats |
| MS1-36-3 | 100.00% | 94.72% | 90.91% | 45.28% | 0.0000% | final stats |
| MS1-36-4 | 100.00% | 95.72% | 92.84% | 45.43% | 0.0000% | final stats |
| MS1-36-5 | 100.00% | 93.82% | 89.88% | 46.52% | 0.0000% | final stats |
| MS1-36-6 | 100.00% | 93.91% | 89.79% | 46.32% | 0.0000% | final stats |
| MS1-41-1 | 100.00% | 94.78% | 91.22% | 46.08% | 0.0000% | final stats |
| MS1-41-2 | 100.00% | 94.07% | 90.30% | 47.47% | 0.0000% | final stats |
| MS1-41-3 | 100.00% | 94.68% | 91.18% | 46.14% | 0.0000% | final stats |
| MS1-41-4 | 100.00% | 94.50% | 91.29% | 46.55% | 0.0000% | final stats |
| MS1-41-5 | 100.00% | 94.10% | 90.61% | 47.18% | 0.0000% | final stats |
| MS1-41-6 | 100.00% | 94.19% | 90.69% | 46.38% | 0.0000% | final stats |
| MS1-56-1 | 100.00% | 94.05% | 90.70% | 46.04% | 0.0000% | final stats |
| MS1-56-2 | 100.00% | 94.17% | 90.72% | 46.51% | 0.0000% | final stats |
| MS1-56-3 | 100.00% | 94.70% | 91.80% | 46.41% | 0.0000% | final stats |
| MS1-56-4 | 100.00% | 95.36% | 92.56% | 46.50% | 0.0000% | final stats |
| MS1-56-5 | 100.00% | 92.66% | 88.84% | 49.44% | 0.0000% | final stats |
| MS1-56-6 | 100.00% | 94.45% | 91.09% | 46.94% | 0.0000% | final stats |
| STJM-4-1 | 100.00% | 90.04% | 84.28% | 50.21% | 0.0000% | final stats |
| STJM-4-2 | 100.00% | 93.27% | 89.48% | 47.37% | 0.0000% | final stats |
| STJM-4-3 | 100.00% | 92.42% | 87.08% | 46.87% | 0.0000% | final stats |
| STJM-4-4 | 100.00% | 94.28% | 90.76% | 47.31% | 0.0000% | final stats |
| STJM-4-5 | 100.00% | 91.91% | 86.87% | 47.89% | 0.0000% | final stats |
| STJM-4-6 | 100.00% | 93.30% | 88.29% | 47.82% | 0.0000% | final stats |
Read Lengths: Paired End
Distribution of read lengths for each sample.
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Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.
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Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
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