Sample Subject_ID Cell_Type Genotype Age Sex Treatment Total_reads Uniq_Rate Multi_Rate Unmap_Rate Uniq_Mapped_Reads Gene_Rate Ambiguity_Rate No_Feature_Rate Avg_Corr Corr_diff MADScore isOutlier Pct_MT Pct_Top1 Pct_Top10
2mo-WT-10F subject10 Microglia WT 2m F None 18904359 86.61 4.36 9.03 16372249 81.15 4.11 14.74 0.86 0 -0.36 N 0 5.7 16
2mo-WT-11F subject11 Microglia WT 2m F None 17493577 87.71 4.2 8.09 15343279 81.36 4.04 14.6 0.86 0 -0.63 N 0 5.6 16
2mo-WT-6F subject6 Microglia WT 2m F None 19200414 86.53 4.56 8.91 16615030 83.59 4.19 12.21 0.86 -0.01 -1.3 N 0 6.1 16.3
2mo-WT-7F subject7 Microglia WT 2m F None 19854165 84.06 4.65 11.29 16688759 76.05 3.87 20.09 0.85 -0.01 -2.38 N 0 5.8 16
2mo-WT-8F subject8 Microglia WT 2m F None 16939381 85.06 4.2 10.74 14409067 77.23 3.88 18.89 0.85 -0.01 -2.73 N 0 5.5 15.8
2mo-WT-9F subject9 Microglia WT 2m F None 18299805 86.42 4.62 8.96 15815434 74.09 3.85 22.06 0.86 -0.01 -1.51 N 0 5.4 16
2mo-WT-1M subject1 Microglia WT 2m M None 18946075 87.09 4.34 8.57 16501047 81.14 4 14.87 0.86 -0.01 -1.56 N 0 5.6 15.6
2mo-WT-2M subject2 Microglia WT 2m M None 20410378 87.58 4.3 8.12 17875410 81.09 3.88 15.03 0.86 0 -1.21 N 0 5.6 15.5
2mo-WT-3M subject3 Microglia WT 2m M None 19467088 86.91 4.32 8.77 16919219 79.05 3.9 17.05 0.86 0 -1.12 N 0 5.5 15.6
2mo-WT-4M subject4 Microglia WT 2m M None 20159788 85.92 4.47 9.61 17321568 77.6 3.88 18.52 0.85 -0.01 -1.98 N 0 5.6 15.6
2mo-WT-5M subject5 Microglia WT 2m M None 19610035 85.04 4.67 10.29 16675780 75.17 3.83 20.99 0.85 -0.02 -3.19 N 0 5.3 15.7
2mo-Het-3F subject14 Microglia Het 2m F None 19497928 87.88 4.16 7.96 17134687 80.78 4 15.21 0.87 0.01 0.56 N 0 5.2 15.3
2mo-Het-4F subject15 Microglia Het 2m F None 19409670 87.86 4.21 7.93 17053063 81.59 4.02 14.39 0.87 0.01 0.8 N 0 5.3 15.4
2mo-Het-5F subject16 Microglia Het 2m F None 16006610 85.59 4.59 9.82 13700572 76.9 3.92 19.19 0.86 -0.01 -1.71 N 0 5.5 15.8
2mo-Het-6F subject17 Microglia Het 2m F None 19763628 81.17 4.29 14.54 16042900 73.12 3.67 23.22 0.84 -0.02 -4.36 N 0 5.1 15.4
2mo-Het-10M subject20 Microglia Het 2m M None 20411729 85.03 4.62 10.35 17355249 72.3 3.65 24.05 0.85 -0.01 -2.81 N 0 5.4 15.5
2mo-Het-1M subject12 Microglia Het 2m M None 17535354 87.77 4.18 8.05 15390432 82.08 3.96 13.96 0.87 0 0.4 N 0 5.7 16
2mo-Het-2M subject13 Microglia Het 2m M None 21188747 87.98 4.2 7.82 18642144 81.19 3.9 14.9 0.87 0.01 0.79 N 0 5.6 15.7
2mo-Het-7M subject18 Microglia Het 2m M None 20134597 87.17 4.25 8.58 17551946 78.84 3.96 17.2 0.86 0 -0.41 N 0 5.3 15.8
2mo-Het-9M subject19 Microglia Het 2m M None 20124468 85.83 4.41 9.76 17272934 72.85 3.66 23.49 0.85 -0.01 -1.74 N 0 4.7 14.9
2mo-KO-4F subject22 Microglia KO 2m F None 18814759 87.07 4.37 8.56 16382307 80.64 4.03 15.34 0.87 0 0.28 N 0 5.6 16.4
2mo-KO-5F subject23 Microglia KO 2m F None 20077421 87.29 4.33 8.38 17526561 79.88 4.03 16.09 0.87 0.01 0.55 N 0 5.6 16.5
2mo-KO-6F subject24 Microglia KO 2m F None 16767338 87.55 4.28 8.17 14680314 80.76 3.93 15.31 0.87 0 0.38 N 0 5.3 15.8
2mo-KO-7F subject25 Microglia KO 2m F None 20683636 81.84 5.01 13.15 16926596 70.16 4.05 25.79 0.84 -0.03 -4.81 N 0 8.3 22.3
2mo-KO-8F subject26 Microglia KO 2m F None 19724601 82 4.93 13.07 16173400 72.25 4.04 23.71 0.84 -0.02 -4.1 N 0 7.8 21.4
2mo-KO-10M subject28 Microglia KO 2m M None 18391624 87.47 4.24 8.29 16087876 78.82 3.9 17.29 0.87 0 0.26 N 0 5.3 15.7
2mo-KO-11M subject29 Microglia KO 2m M None 16936299 87.28 4.35 8.37 14782758 79.75 4.01 16.24 0.86 0 -0.47 N 0 5.1 15.7
2mo-KO-12M subject30 Microglia KO 2m M None 18454148 87.78 4.22 8 16199371 81.99 4.05 13.96 0.86 0 -0.08 N 0 5 15.5
2mo-KO-13M subject31 Microglia KO 2m M None 17300935 85.69 4.55 9.76 14824552 75 3.84 21.16 0.86 0 -0.74 N 0 4.8 15.5
2mo-KO-2M subject21 Microglia KO 2m M None 21436635 81.99 4.62 13.39 17576281 79.45 3.9 16.66 0.85 -0.02 -3.11 N 0 7.2 18.3
2mo-KO-9M subject27 Microglia KO 2m M None 21016096 87.29 4.31 8.4 18343959 82.5 4.05 13.45 0.87 0.01 0.54 N 0 5.3 15.7
1yr-WT-2F subject32 Microglia WT 1y F None 19808357 87.33 4.02 8.65 17298416 77.95 3.75 18.3 0.86 0 -0.04 N 0 5.1 15.2
1yr-WT-3F subject33 Microglia WT 1y F None 17032558 86.06 4.18 9.76 14658644 76.65 4.02 19.33 0.86 0 -0.78 N 0 6.1 17.2
1yr-WT-4F subject34 Microglia WT 1y F None 18902841 85.89 4.24 9.87 16236112 79.16 4.02 16.82 0.86 0 0 N 0 5.6 16.3
1yr-WT-5F subject35 Microglia WT 1y F None 18201876 84.97 4.29 10.74 15466401 77.39 4.06 18.56 0.86 0 -0.98 N 0 5.9 17
1yr-WT-6F subject36 Microglia WT 1y F None 19423623 87.76 4.14 8.1 17046198 80.16 3.91 15.93 0.87 0.01 0.84 N 0 5.2 15.4
1yr-WT-7F subject37 Microglia WT 1y F None 16657329 85.53 4.31 10.16 14247664 82.17 3.99 13.84 0.86 0 -0.3 N 0 5.5 15.6
1yr-WT-8F subject38 Microglia WT 1y F None 17939667 86.5 4.18 9.32 15518410 81.41 3.92 14.67 0.87 0 0.12 N 0 5.3 15.4
1yr-WT-10M subject40 Microglia WT 1y M None 16949235 81.65 4.35 14 13839846 85.24 4.19 10.56 0.85 -0.01 -2.16 N 0 4.9 15.6
1yr-WT-11M subject41 Microglia WT 1y M None 16712616 81.85 4.63 13.52 13679842 83.56 4.28 12.17 0.86 -0.01 -1.33 N 0 6.5 17.2
1yr-WT-9M subject39 Microglia WT 1y M None 18634879 81.95 4.44 13.61 15271321 83.67 4.18 12.15 0.86 0 -1.27 N 0 6 16.4
1yr-Het-1F subject42 Microglia Het 1y F None 21114493 83.14 4.68 12.18 17554839 78.92 4.31 16.77 0.86 -0.01 -1.67 N 0 6.6 19.6
1yr-Het-5F subject45 Microglia Het 1y F None 17900099 86.76 4.01 9.23 15530330 77.23 3.9 18.87 0.86 0 -0.73 N 0 5.3 16.2
1yr-Het-6F subject46 Microglia Het 1y F None 13932054 84.72 3.96 11.32 11802922 78.06 3.84 18.1 0.85 -0.01 -2.2 N 0 5.2 15.5
1yr-Het-7F subject47 Microglia Het 1y F None 16171291 86.01 4.36 9.63 13909217 81.04 4.08 14.88 0.86 0 -0.94 N 0 5.4 15.9
1yr-Het-8F subject48 Microglia Het 1y F None 16421962 81.11 4.26 14.63 13319104 78.6 4.12 17.28 0.85 -0.01 -2.86 N 0 6.4 17.5
1yr-Het-9F subject49 Microglia Het 1y F None 18563912 86.28 4.37 9.35 16016812 78.6 4.11 17.3 0.87 0 0.21 N 0 5.8 16.8
1yr-Het-11M subject50 Microglia Het 1y M None 20381975 86.91 4.22 8.87 17713708 79.19 3.91 16.9 0.87 0.01 0.56 N 0 5.3 15.6
1yr-Het-12M subject51 Microglia Het 1y M None 19063364 86.9 4.32 8.78 16566834 80.91 3.96 15.12 0.87 0.01 0.66 N 0 5.1 15.3
1yr-Het-14M subject52 Microglia Het 1y M None 18020616 83.25 4.39 12.36 15001438 78.5 3.97 17.53 0.86 -0.01 -1.42 N 0 6 16.4
1yr-Het-2M subject43 Microglia Het 1y M None 17463825 86.8 4.37 8.83 15158429 82.76 4.13 13.11 0.87 0.01 0.65 N 0 5.8 16.3
1yr-Het-4M subject44 Microglia Het 1y M None 18192458 86.25 4.32 9.43 15690329 82.52 4.06 13.42 0.87 0 0.02 N 0 5.4 15.6
1yr-KO-11F subject60 Microglia KO 1y F None 18046260 84.21 4.36 11.43 15195932 76.42 4.1 19.48 0.85 -0.01 -1.73 N 0 5.8 17.7
1yr-KO-1F subject53 Microglia KO 1y F None 17424405 85.32 4.24 10.44 14866900 80.97 4.14 14.89 0.86 0 -0.83 N 0 5.3 16.2
1yr-KO-2F subject54 Microglia KO 1y F None 16872280 87.2 4.11 8.69 14712961 79.43 3.99 16.58 0.87 0.01 0.53 N 0 5 15.9
1yr-KO-3F subject59 Microglia KO 1y F None 18603109 87.41 4.09 8.5 16261290 79.51 3.94 16.54 0.87 0 0.36 N 0 5 15.8
1yr-KO-8F subject57 Microglia KO 1y F None 15802629 87.03 4 8.97 13753152 77.34 3.96 18.7 0.86 0 -0.64 N 0 4.9 16.1
1yr-KO-9F subject58 Microglia KO 1y F None 20380665 85.45 4.01 10.54 17415918 78.72 3.98 17.3 0.86 0 -0.61 N 0 5.1 16
1yr-KO-13M subject61 Microglia KO 1y M None 17885226 87.14 4.49 8.37 15584300 82.43 4.02 13.55 0.87 0.01 0.84 N 0 5.6 15.9
1yr-KO-14M subject62 Microglia KO 1y M None 17455616 87.21 4.31 8.48 15222772 81.25 4.01 14.74 0.87 0 0.03 N 0 5.7 16.2
1yr-KO-15M subject63 Microglia KO 1y M None 17160388 84.93 4.48 10.59 14575101 80.1 4 15.91 0.86 0 -0.43 N 0 6 16.6
1yr-KO-16M subject64 Microglia KO 1y M None 16889153 86.82 4.55 8.63 14662521 80.92 4.08 15.01 0.87 0.01 0.8 N 0 6 16.8
1yr-KO-6M subject55 Microglia KO 1y M None 17808713 86.34 4.4 9.26 15376813 81.65 4.17 14.18 0.87 0.01 0.5 N 0 5.8 16.8
1yr-KO-7M subject56 Microglia KO 1y M None 18033050 86.37 4.44 9.19 15574468 82.48 4.22 13.3 0.87 0.01 0.42 N 0 5.9 16.8
2yr-WT-1F subject65 Microglia WT 2y F None 17020684 88.74 4.22 7.04 15104610 80.31 3.93 15.75 0.87 0.01 0.42 N 0 5.7 16.1
2yr-WT-2F subject66 Microglia WT 2y F None 20941407 88.34 4.52 7.14 18499821 78.56 3.79 17.65 0.85 -0.02 -3.39 N 0 2.3 12.3
2yr-WT-3F subject67 Microglia WT 2y F None 19720881 88.98 3.98 7.04 17548308 80.25 3.93 15.82 0.87 0.01 0.67 N 0 5 15.6
2yr-WT-5F subject69 Microglia WT 2y F None 19582557 88.92 4.07 7.01 17412057 81.66 4.08 14.26 0.87 0.01 1.24 N 0 5.4 16
2yr-WT-6F subject70 Microglia WT 2y F None 18077234 88.98 4.2 6.82 16084476 82.75 4.12 13.12 0.87 0.01 0.96 N 0 5.2 15.8
2yr-WT-7F subject71 Microglia WT 2y F None 17340488 88.6 4.04 7.36 15364196 76.22 3.87 19.91 0.86 0 -0.17 N 0 4.8 16
2yr-WT-8F subject72 Microglia WT 2y F None 19379696 87.82 4.02 8.16 17019475 79.19 3.88 16.93 0.86 0 -0.24 N 0 5.5 16.7
2yr-WT-10M subject74 Microglia WT 2y M None 20347211 88.11 4.1 7.79 17928722 79.41 3.82 16.77 0.87 0.01 0.49 N 0 5.7 15.8
2yr-WT-4M subject68 Microglia WT 2y M None 20107699 88.29 4.48 7.23 17752454 84.33 4.1 11.57 0.87 0.01 0.51 N 0 6 15.8
2yr-WT-9M subject73 Microglia WT 2y M None 17439361 88.58 4.1 7.32 15447393 79.97 3.99 16.04 0.87 0.01 0.55 N 0 5.6 16.1
2yr-Het-2F subject76 Microglia Het 2y F None 19297319 89.01 4.05 6.94 17176402 81.33 4.04 14.63 0.87 0.01 1.04 N 0 4.7 15.3
2yr-Het-6F subject80 Microglia Het 2y F None 20159656 88.7 4.22 7.08 17882005 83.5 4.15 12.35 0.87 0.01 1.62 N 0 5.2 15.7
2yr-Het-7F subject81 Microglia Het 2y F None 15727421 88.62 4.07 7.31 13937158 80.34 4.02 15.64 0.86 0 -0.04 N 0 5.2 15.9
2yr-Het-8F subject82 Microglia Het 2y F None 19493535 88.1 3.74 8.16 17172903 77.95 3.84 18.21 0.86 0 -0.56 N 0 4.1 15.2
2yr-Het-1M subject75 Microglia Het 2y M None 19783560 88.9 4.14 6.96 17586721 82.53 4.02 13.45 0.87 0.01 0.95 N 0 5.2 15.4
2yr-Het-3M subject77 Microglia Het 2y M None 20167126 88.9 4.04 7.06 17928560 82.35 4.16 13.49 0.87 0.01 0.84 N 0 5.2 15.7
2yr-Het-4M subject78 Microglia Het 2y M None 18062534 88.03 4.18 7.79 15901281 81.5 3.91 14.59 0.87 0 0.24 N 0 5.6 15.6
2yr-Het-5M subject79 Microglia Het 2y M None 17678455 88.84 4.15 7.01 15704938 83.69 4.13 12.19 0.87 0.01 0.45 N 0 5.4 15.7
2yr-KO-4F subject86 Microglia KO 2y F None 17948917 88.4 3.98 7.62 15867419 81 4.09 14.91 0.86 0 -0.37 N 0 4.7 15.7
2yr-KO-7F subject88 Microglia KO 2y F None 18285075 88.02 4.21 7.77 16094595 81.91 4.3 13.79 0.87 0.01 0.79 N 0 5.8 17.3
2yr-KO-8F subject89 Microglia KO 2y F None 16300273 88.42 4.23 7.35 14411987 80.51 4.1 15.39 0.87 0 0.26 N 0 4.9 15.8
2yr-KO-9F subject90 Microglia KO 2y F None 17901668 87.66 4.33 8.01 15691754 79.75 4.2 16.05 0.87 0.01 0.75 N 0 5.7 16.9
2yr-KO-10M subject91 Microglia KO 2y M None 17925995 88.12 4.22 7.66 15796332 81.96 4.14 13.9 0.87 0.01 0.62 N 0 5.6 16.5
2yr-KO-11M subject92 Microglia KO 2y M None 19272100 88.28 4.38 7.34 17013855 86.1 4.37 9.52 0.87 0.01 1.19 N 0 6.1 16.9
2yr-KO-12M subject93 Microglia KO 2y M None 17534985 87.97 4.26 7.77 15424747 80.25 3.91 15.83 0.87 0.01 0.7 N 0 5.6 15.9
2yr-KO-1M subject83 Microglia KO 2y M None 18233801 88.85 4.21 6.94 16199966 83.06 4.33 12.61 0.87 0 0.28 N 0 4.1 16.1
2yr-KO-2M subject84 Microglia KO 2y M None 17427145 88.88 4.04 7.08 15489932 80.87 4.05 15.08 0.87 0 0.36 N 0 5 16.2
2yr-KO-3M subject85 Microglia KO 2y M None 17941729 88.63 4.04 7.33 15902643 80.27 3.91 15.81 0.87 0.01 0.49 N 0 5.4 15.7
2yr-KO-6M subject87 Microglia KO 2y M None 17913519 88.52 4.08 7.4 15857793 79.36 3.94 16.7 0.87 0.01 0.66 N 0 5.5 16.3
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Total number of sequencing reads from raw fastq file
Percentage of reads uniquely mapped to the reference genome.
Percentage of reads mapped equally well to multiple locations on the reference genome.
Percentage of reads not mapped to the reference genome.
Number of uniquely mapped reads.
Percentage of reads mapped to unique gene region, including Exons, UTRs and Introns.
Percentage of reads mapped to gene-overlapping region and can't be unambiguously assigned to either gene.
Percentage of reads mapped to unannotated genomic regions.
Percentage of mapped reads on Exons.
Percentage of mapped reads on 5' UTR.
Percentage of mapped reads on 3' UTR.
Percentage of mapped reads on Introns.
Percentage of mapped reads on Intergenic regions.
Reads counted by featureCounts (=uniquely mapped read * uniq_rate)
Normalization factor calculated by edgeR
Average correlation where this sample is involved
Avg_Corr : Average correlation where this sample is involved;
Avg_Rest : Average correlation where this sample is NOT involved;
Corr_diff : The difference between Avg_Corr and Avg_Rest.
(1) For each sample, calculate the correlation difference. This is simply a difference between the average of all the pair wise correlations that involve the sample (for the same group) and the average of all the pair wise correlations that do not involve the sample. For example, if we have a, b, c, d for group 1, the correlation difference of sample a is:
The difference of Average (correlation(a, b), correlation(a, c), correlation(a, d)) and Average (correlation(b, c), correlation (b, d), correlation(c, d)). You can see that if sample a is an outlier, then the difference will be negative.
(2) Now we have a vector of values (one for each sample). We simply convert this vector to MAD scores (robust Z-scores) by subtracting the medians then dividing it by median absolute deviations (MAD). We use a standard MAD cutoff (e.g. -5) to determine the outliers.