TRAX Data Quality Report
Date: Friday June 12, 2020
Run mode: tRNA fragments
In ARMSeq mode for tRNA fragment analysis
Summary
Passed Mappable reads > 200000 (mousearmseqpaper-mapinfo.pdf)
Passed Mapping rate > 65.0% (mousearmseqpaper-mapinfo.pdf)
Warning tRNA read share > 5.0% (mousearmseqpaper-typecounts.pdf)
Warning rRNA read share < 35.0% (mousearmseqpaper-typecounts.pdf)
Warning Reads mapping to unannotated regions < 35.0% (mousearmseqpaper-typecounts.pdf)
Warning Read length average < 40 bases (mousearmseqpaper-readlengths.pdf)
Warning < 70.0% of reads between 15 and 50 bases (mousearmseqpaper-readlengths.pdf)
Passed < 50.0% of tRNAs with more than 20 reads (mousearmseqpaper-tRNAcounts.txt)
Warning DESeq2 sizefactor differences < 3.0x (mousearmseqpaper-SizeFactors.txt)
Mappable reads > 200000
| Status | Sample | Read Count |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 3605295.00 |
| Passed | M_dm_Brain_M5_plusAlkB | 3728088.00 |
| Passed | M_dm_Brain_M6_plusAlkB | 3238746.00 |
| Passed | ARMseq_AlkB_Heart_1 | 917248.00 |
| Passed | ARMseq_AlkB_Heart_2 | 859414.00 |
| Passed | ARMseq_AlkB_Heart_3 | 968771.00 |
| Passed | AlkB_Liver_1 | 790282.00 |
| Passed | AlkB_Liver_2 | 847688.00 |
| Passed | M_dm_Brain_M4_minusAlkB | 2537337.00 |
| Passed | M_dm_Brain_M5_minusAlkB | 3351770.00 |
| Passed | M_dm_Brain_M6_minusAlkB | 2763590.00 |
| Passed | ARMseq_Heart_1 | 709260.00 |
| Passed | ARMseq_Heart_2 | 932665.00 |
| Passed | ARMseq_Heart_3 | 963151.00 |
| Passed | Liver_1 | 987480.00 |
| Passed | Liver_2 | 1060908.00 |
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Mapping rate > 65.0%
| Status | Sample | Mapping Rate |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 93.74% |
| Passed | M_dm_Brain_M5_plusAlkB | 94.02% |
| Passed | M_dm_Brain_M6_plusAlkB | 93.64% |
| Passed | ARMseq_AlkB_Heart_1 | 92.38% |
| Passed | ARMseq_AlkB_Heart_2 | 90.39% |
| Passed | ARMseq_AlkB_Heart_3 | 89.83% |
| Passed | AlkB_Liver_1 | 88.45% |
| Passed | AlkB_Liver_2 | 87.91% |
| Passed | M_dm_Brain_M4_minusAlkB | 93.19% |
| Passed | M_dm_Brain_M5_minusAlkB | 94.10% |
| Passed | M_dm_Brain_M6_minusAlkB | 93.83% |
| Passed | ARMseq_Heart_1 | 89.62% |
| Passed | ARMseq_Heart_2 | 90.03% |
| Passed | ARMseq_Heart_3 | 88.22% |
| Passed | Liver_1 | 87.89% |
| Passed | Liver_2 | 87.42% |
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tRNA read share > 5.0%
| Status | Sample | tRNA Read Percentage |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 13.82% |
| Passed | M_dm_Brain_M5_plusAlkB | 16.48% |
| Passed | M_dm_Brain_M6_plusAlkB | 12.97% |
| Passed | ARMseq_AlkB_Heart_1 | 14.57% |
| Passed | ARMseq_AlkB_Heart_2 | 13.30% |
| Passed | ARMseq_AlkB_Heart_3 | 13.69% |
| Passed | AlkB_Liver_1 | 13.84% |
| Passed | AlkB_Liver_2 | 16.61% |
| Warning | M_dm_Brain_M4_minusAlkB | 4.66% |
| Warning | M_dm_Brain_M5_minusAlkB | 4.06% |
| Passed | M_dm_Brain_M6_minusAlkB | 5.11% |
| Passed | ARMseq_Heart_1 | 7.42% |
| Passed | ARMseq_Heart_2 | 8.67% |
| Passed | ARMseq_Heart_3 | 8.18% |
| Passed | Liver_1 | 5.80% |
| Passed | Liver_2 | 7.61% |
back to Summary
rRNA read share < 35.0%
| Status | Sample | rRNA Read Percentage |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 24.34% |
| Passed | M_dm_Brain_M5_plusAlkB | 28.32% |
| Passed | M_dm_Brain_M6_plusAlkB | 30.22% |
| Passed | ARMseq_AlkB_Heart_1 | 14.28% |
| Passed | ARMseq_AlkB_Heart_2 | 18.58% |
| Passed | ARMseq_AlkB_Heart_3 | 18.18% |
| Passed | AlkB_Liver_1 | 34.66% |
| Passed | AlkB_Liver_2 | 31.26% |
| Passed | M_dm_Brain_M4_minusAlkB | 32.98% |
| Passed | M_dm_Brain_M5_minusAlkB | 29.65% |
| Passed | M_dm_Brain_M6_minusAlkB | 28.62% |
| Passed | ARMseq_Heart_1 | 17.34% |
| Passed | ARMseq_Heart_2 | 18.79% |
| Passed | ARMseq_Heart_3 | 17.42% |
| Warning | Liver_1 | 38.05% |
| Passed | Liver_2 | 31.90% |
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Reads mapping to unannotated regions < 35.0%
| Status | Sample | Unannotated Region Mapping Rate |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 13.96% |
| Passed | M_dm_Brain_M5_plusAlkB | 12.06% |
| Passed | M_dm_Brain_M6_plusAlkB | 13.39% |
| Passed | ARMseq_AlkB_Heart_1 | 32.03% |
| Passed | ARMseq_AlkB_Heart_2 | 31.59% |
| Passed | ARMseq_AlkB_Heart_3 | 31.93% |
| Passed | AlkB_Liver_1 | 34.63% |
| Passed | AlkB_Liver_2 | 34.76% |
| Passed | M_dm_Brain_M4_minusAlkB | 13.71% |
| Passed | M_dm_Brain_M5_minusAlkB | 12.80% |
| Passed | M_dm_Brain_M6_minusAlkB | 13.70% |
| Warning | ARMseq_Heart_1 | 37.03% |
| Passed | ARMseq_Heart_2 | 33.24% |
| Warning | ARMseq_Heart_3 | 37.84% |
| Warning | Liver_1 | 39.58% |
| Warning | Liver_2 | 42.42% |
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Read length average < 40 bases
| Status | Sample | Average Read Length |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 39.49 |
| Warning | M_dm_Brain_M5_plusAlkB | 40.95 |
| Warning | M_dm_Brain_M6_plusAlkB | 42.69 |
| Passed | ARMseq_AlkB_Heart_1 | 32.06 |
| Passed | ARMseq_AlkB_Heart_2 | 32.10 |
| Passed | ARMseq_AlkB_Heart_3 | 32.68 |
| Passed | AlkB_Liver_1 | 31.25 |
| Passed | AlkB_Liver_2 | 32.09 |
| Passed | M_dm_Brain_M4_minusAlkB | 35.99 |
| Passed | M_dm_Brain_M5_minusAlkB | 34.96 |
| Passed | M_dm_Brain_M6_minusAlkB | 35.81 |
| Passed | ARMseq_Heart_1 | 24.56 |
| Passed | ARMseq_Heart_2 | 23.91 |
| Passed | ARMseq_Heart_3 | 23.70 |
| Passed | Liver_1 | 24.47 |
| Passed | Liver_2 | 23.18 |
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< 70.0% of reads between 15 and 50 bases
| Status | Sample | Read Percentage |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 73.02% |
| Warning | M_dm_Brain_M5_plusAlkB | 65.84% |
| Warning | M_dm_Brain_M6_plusAlkB | 61.88% |
| Passed | ARMseq_AlkB_Heart_1 | 83.18% |
| Passed | ARMseq_AlkB_Heart_2 | 81.66% |
| Passed | ARMseq_AlkB_Heart_3 | 81.85% |
| Passed | AlkB_Liver_1 | 85.99% |
| Passed | AlkB_Liver_2 | 82.69% |
| Passed | M_dm_Brain_M4_minusAlkB | 87.91% |
| Passed | M_dm_Brain_M5_minusAlkB | 88.28% |
| Passed | M_dm_Brain_M6_minusAlkB | 87.66% |
| Passed | ARMseq_Heart_1 | 93.81% |
| Passed | ARMseq_Heart_2 | 93.65% |
| Passed | ARMseq_Heart_3 | 93.86% |
| Passed | Liver_1 | 94.75% |
| Passed | Liver_2 | 94.83% |
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< 50.0% of tRNAs with more than 20 reads
| Status | Sample | Percentage of tRNAs |
|---|
| Passed | M_dm_Brain_M4_plusAlkB | 97.71% |
| Passed | M_dm_Brain_M5_plusAlkB | 97.71% |
| Passed | M_dm_Brain_M6_plusAlkB | 97.71% |
| Passed | ARMseq_AlkB_Heart_1 | 97.71% |
| Passed | ARMseq_AlkB_Heart_2 | 97.71% |
| Passed | ARMseq_AlkB_Heart_3 | 97.71% |
| Passed | AlkB_Liver_1 | 97.71% |
| Passed | AlkB_Liver_2 | 97.71% |
| Passed | M_dm_Brain_M4_minusAlkB | 97.71% |
| Passed | M_dm_Brain_M5_minusAlkB | 97.71% |
| Passed | M_dm_Brain_M6_minusAlkB | 97.71% |
| Passed | ARMseq_Heart_1 | 97.71% |
| Passed | ARMseq_Heart_2 | 97.71% |
| Passed | ARMseq_Heart_3 | 97.71% |
| Passed | Liver_1 | 97.71% |
| Passed | Liver_2 | 97.71% |
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DESeq2 sizefactor differences < 3.0x
| Status | Sample | Size Factor |
|---|
| Warning | M_dm_Brain_M4_plusAlkB | 3.86 |
| Warning | M_dm_Brain_M5_plusAlkB | 4.30 |
| Warning | M_dm_Brain_M6_plusAlkB | 3.07 |
| Passed | ARMseq_AlkB_Heart_1 | 0.53 |
| Passed | ARMseq_AlkB_Heart_2 | 0.46 |
| Passed | ARMseq_AlkB_Heart_3 | 0.58 |
| Passed | AlkB_Liver_1 | 0.55 |
| Passed | AlkB_Liver_2 | 0.65 |
| Passed | M_dm_Brain_M4_minusAlkB | 1.76 |
| Passed | M_dm_Brain_M5_minusAlkB | 2.48 |
| Passed | M_dm_Brain_M6_minusAlkB | 2.13 |
| Passed | ARMseq_Heart_1 | 0.43 |
| Passed | ARMseq_Heart_2 | 0.58 |
| Passed | ARMseq_Heart_3 | 0.56 |
| Passed | Liver_1 | 0.52 |
| Passed | Liver_2 | 0.66 |
back to Summary