Noi/NOTES/2011-3-17
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Data analysis of sequencing library of Parkinson's patient samples from Burnham Institute
- Sequencing library ID: NP-220K-Parkinson_Ind1-18-Feb15, HL089 run
- Library construction: [[1]]
Sample information
Pair | Control Sample ID | Sample code | Sex | age (year.day) | Postmortem time | PD Sample ID | Sample code | Sex | age (year.day) | Postmortem time |
1 | 5028 | P1C | M | 67.293 | P18 | 1947 | P1P | M | 70.251 | P17 |
2 | 4789 | P2C | F | 72.053 | P19 | 4977 | P2P | F | 76.081 | P14 |
3 | 5171 | P3C | M | 79.088 | P05 | 4879 | P3P | M | 75.351 | P15 |
4 | 1818 | P4C | M | 76.294 | P03 | 4526 | P4P | M | 78.182 | P01 |
5 | 5089 | P5C | M | 89.018 | P14 | 5203 | P5P | M | 89.06 | P10 |
6 | 5237 | P6C | M | 52.291 | P13 | 1910 | P6P | M | 51.243 | P10 |
7 | 1569 | P7C1 | F | 77.089 | P08 | 1401 | P7P | F | 80.215 | P04 |
7 | 5219 | P7C2 | F | 76.348 | P03 | |||||
8 | 4735 | P8C | M | 73.184 | P21 | 1741 | P8P1 | M | 71.348 | P20 |
8 | 5306 | P8P2 | M | 76.311 | P21 |
DMR220k mapping by SOAP
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | Combined Mapping Rate |
P1C | P1C_1.txt.fwd.soap.PE.out | 11587217 | 4532458 | 39.12(%) | 75.28% |
P1C_1.txt.rev.soap.PE.out | 11587217 | 4189445 | 36.16(%) | ||
P2C | P2C_1.txt.fwd.soap.PE.out | 15881433 | 6006681 | 37.82(%) | 71.97% |
P2C_1.txt.rev.soap.PE.out | 15881433 | 5422813 | 34.15(%) | ||
P3C | P3C_1.txt.fwd.soap.PE.out | 11143726 | 4292874 | 38.52(%) | 74.06% |
P3C_1.txt.rev.soap.PE.out | 11143726 | 3960855 | 35.54(%) | ||
P4C | P4C_1.txt.fwd.soap.PE.out | 12849788 | 4630353 | 36.03(%) | 69.19% |
P4C_1.txt.rev.soap.PE.out | 12849788 | 4261621 | 33.16(%) | ||
P5C | P5C_1.txt.fwd.soap.PE.out | 14221122 | 5724586 | 40.25(%) | 77.03% |
P5C_1.txt.rev.soap.PE.out | 14221122 | 5230402 | 36.78(%) | ||
P6C | P6C_1.txt.fwd.soap.PE.out | 14112863 | 5168312 | 36.62(%) | 70.35% |
P6C_1.txt.rev.soap.PE.out | 14112863 | 4760129 | 33.73(%) | ||
P7C1 | P7C1_1.txt.fwd.soap.PE.out | 13273426 | 5029339 | 37.89(%) | 72.48% |
P7C1_1.txt.rev.soap.PE.out | 13273426 | 4590775 | 34.59(%) | ||
P7C2 | P7C2_1.txt.fwd.soap.PE.out | 10804019 | 4102770 | 37.97(%) | 73.93% |
P7C2_1.txt.rev.soap.PE.out | 10804019 | 3884944 | 35.96(%) | ||
P8C | P8C_1.txt.fwd.soap.PE.out | 11113577 | 3978002 | 35.79(%) | 68.72% |
P8C_1.txt.rev.soap.PE.out | 11113577 | 3660086 | 32.93(%) | ||
P1P | P1P_1.txt.fwd.soap.PE.out | 11887236 | 4435830 | 37.32(%) | 71.40% |
P1P_1.txt.rev.soap.PE.out | 11887236 | 4051377 | 34.08(%) | ||
P2P | P2P_1.txt.fwd.soap.PE.out | 10570835 | 3719618 | 35.19(%) | 67.49% |
P2P_1.txt.rev.soap.PE.out | 10570835 | 3414342 | 32.30(%) | ||
P3P | P3P_1.txt.fwd.soap.PE.out | 12343982 | 4467880 | 36.19(%) | 69.43% |
P3P_1.txt.rev.soap.PE.out | 12343982 | 4103164 | 33.24(%) | ||
P4P | P4P_1.txt.fwd.soap.PE.out | 13306437 | 4612404 | 34.66(%) | 66.16% |
P4P_1.txt.rev.soap.PE.out | 13306437 | 4191194 | 31.50(%) | ||
P5P | P5P_1.txt.fwd.soap.PE.out | 16356159 | 6335050 | 38.73(%) | 75.05% |
P5P_1.txt.rev.soap.PE.out | 16356159 | 5941194 | 36.32(%) | ||
P6P | P6P_1.txt.fwd.soap.PE.out | 12406211 | 4691026 | 37.81(%) | 72.84% |
P6P_1.txt.rev.soap.PE.out | 12406211 | 4345710 | 35.03(%) | ||
P7P | P7P_1.txt.fwd.soap.PE.out | 14361383 | 5263978 | 36.65(%) | 71.46% |
P7P_1.txt.rev.soap.PE.out | 14361383 | 4998621 | 34.81(%) | ||
P8P1 | P8P1_1.txt.fwd.soap.PE.out | 15686569 | 6074276 | 38.72(%) | 74.48% |
P8P1_1.txt.rev.soap.PE.out | 15686569 | 5608916 | 35.76(%) | ||
P8P2 | P8P2_1.txt.fwd.soap.PE.out | 13317181 | 4960421 | 37.25(%) | 72.68% |
P8P2_1.txt.rev.soap.PE.out | 13317181 | 4718163 | 35.43(%) |
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | Combined Mapping Rate |
P1C | P1C_1.txt.trimmed.fwd.soap.PE.out | 11587217 | 4651950 | 40.15(%) | 77.26% |
P1C_1.txt.trimmed.rev.soap.PE.out | 11587217 | 4300295 | 37.11(%) | ||
P2C | P2C_1.txt.trimmed.fwd.soap.PE.out | 15881433 | 6153226 | 38.74(%) | 73.76% |
P2C_1.txt.trimmed.rev.soap.PE.out | 15881433 | 5562135 | 35.02(%) | ||
P3C | P3C_1.txt.trimmed.fwd.soap.PE.out | 11143726 | 4394150 | 39.43(%) | 75.85% |
P3C_1.txt.trimmed.rev.soap.PE.out | 11143726 | 4058568 | 36.42(%) | ||
P4C | P4C_1.txt.trimmed.fwd.soap.PE.out | 12849788 | 4755798 | 37.01(%) | 71.09% |
P4C_1.txt.trimmed.rev.soap.PE.out | 12849788 | 4379149 | 34.08(%) | ||
P5C | P5C_1.txt.trimmed.fwd.soap.PE.out | 14221122 | 5870051 | 41.28(%) | 79.00% |
P5C_1.txt.trimmed.rev.soap.PE.out | 14221122 | 5363985 | 37.72(%) | ||
P6C | P6C_1.txt.trimmed.fwd.soap.PE.out | 14112863 | 5300550 | 37.56(%) | 72.17% |
P6C_1.txt.trimmed.rev.soap.PE.out | 14112863 | 4884889 | 34.61(%) | ||
P7C1 | P7C1_1.txt.trimmed.fwd.soap.PE.out | 13273426 | 5153728 | 38.83(%) | 74.30% |
P7C1_1.txt.trimmed.rev.soap.PE.out | 13273426 | 4708161 | 35.47(%) | ||
P7C2 | P7C2_1.txt.trimmed.fwd.soap.PE.out | 10804019 | 4203376 | 38.91(%) | 75.75% |
P7C2_1.txt.trimmed.rev.soap.PE.out | 10804019 | 3980496 | 36.84(%) | ||
P8C | P8C_1.txt.trimmed.fwd.soap.PE.out | 11113577 | 4087969 | 36.78(%) | 70.64% |
P8C_1.txt.trimmed.rev.soap.PE.out | 11113577 | 3763353 | 33.86(%) | ||
P1P | P1P_1.txt.trimmed.fwd.soap.PE.out | 11887236 | 4553543 | 38.31(%) | 73.35% |
P1P_1.txt.trimmed.rev.soap.PE.out | 11887236 | 4165062 | 35.04(%) | ||
P2P | P2P_1.txt.trimmed.fwd.soap.PE.out | 10570835 | 3823742 | 36.17(%) | 69.41% |
P2P_1.txt.trimmed.rev.soap.PE.out | 10570835 | 3513607 | 33.24(%) | ||
P3P | P3P_1.txt.trimmed.fwd.soap.PE.out | 12343982 | 4596931 | 37.24(%) | 71.48% |
P3P_1.txt.trimmed.rev.soap.PE.out | 12343982 | 4226905 | 34.24(%) | ||
P4P | P4P_1.txt.trimmed.fwd.soap.PE.out | 13306437 | 4737667 | 35.60(%) | 67.98% |
P4P_1.txt.trimmed.rev.soap.PE.out | 13306437 | 4308188 | 32.38(%) | ||
P5P | P5P_1.txt.trimmed.fwd.soap.PE.out | 16356159 | 6501010 | 39.75(%) | 77.01% |
P5P_1.txt.trimmed.rev.soap.PE.out | 16356159 | 6094805 | 37.26(%) | ||
P6P | P6P_1.txt.trimmed.fwd.soap.PE.out | 12406211 | 4811998 | 38.79(%) | 74.75% |
P6P_1.txt.trimmed.rev.soap.PE.out | 12406211 | 4460799 | 35.96(%) | ||
P7P | P7P_1.txt.trimmed.fwd.soap.PE.out | 14361383 | 5407295 | 37.65(%) | 73.39% |
P7P_1.txt.trimmed.rev.soap.PE.out | 14361383 | 5132459 | 35.74(%) | ||
P8P1 | P8P1_1.txt.trimmed.fwd.soap.PE.out | 15686569 | 6216980 | 39.63(%) | 76.25% |
P8P1_1.txt.trimmed.rev.soap.PE.out | 15686569 | 5744721 | 36.62(%) | ||
P8P2 | P8P2_1.txt.trimmed.fwd.soap.PE.out | 13317181 | 5099724 | 38.29(%) | 74.65% |
P8P2_1.txt.trimmed.rev.soap.PE.out | 13317181 | 4841963 | 36.36(%) |