Noi/NOTES/2011-3-17: Difference between revisions
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| align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' | | align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' | ||
|- | |- | ||
| P1C||P1C_1.txt.fwd.soap.PE.out||11587217||4532458||39.12||75.28 | | 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|| | | ||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||P2C_1.txt.fwd.soap.PE.out||15881433||6006681||37.82||71.97% | ||
|- | |- | ||
| ||P2C_1.txt.rev.soap.PE.out||15881433||5422813||34.15|| | | ||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||P3C_1.txt.fwd.soap.PE.out||11143726||4292874||38.52||74.06% | ||
|- | |- | ||
| ||P3C_1.txt.rev.soap.PE.out||11143726||3960855||35.54|| | | ||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||P4C_1.txt.fwd.soap.PE.out||12849788||4630353||36.03||69.19% | ||
|- | |- | ||
| ||P4C_1.txt.rev.soap.PE.out||12849788||4261621||33.16|| | | ||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||P5C_1.txt.fwd.soap.PE.out||14221122||5724586||40.25||77.03% | ||
|- | |- | ||
| ||P5C_1.txt.rev.soap.PE.out||14221122||5230402||36.78|| | | ||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||P6C_1.txt.fwd.soap.PE.out||14112863||5168312||36.62||70.35% | ||
|- | |- | ||
| ||P6C_1.txt.rev.soap.PE.out||14112863||4760129||33.73|| | | ||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||P7C1_1.txt.fwd.soap.PE.out||13273426||5029339||37.89||72.48% | ||
|- | |- | ||
| ||P7C1_1.txt.rev.soap.PE.out||13273426||4590775||34.59|| | | ||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||P7C2_1.txt.fwd.soap.PE.out||10804019||4102770||37.97||73.93% | ||
|- | |- | ||
| ||P7C2_1.txt.rev.soap.PE.out||10804019||3884944||35.96|| | | ||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||P8C_1.txt.fwd.soap.PE.out||11113577||3978002||35.79||68.72% | ||
|- | |- | ||
| ||P8C_1.txt.rev.soap.PE.out||11113577||3660086||32.93|| | | ||P8C_1.txt.rev.soap.PE.out||11113577||3660086||32.93|| | ||
|- | |- | ||
| P1P||P1P_1.txt.fwd.soap.PE.out||11887236||4435830||37.32||71.4 | | P1P||P1P_1.txt.fwd.soap.PE.out||11887236||4435830||37.32||71.4% | ||
|- | |- | ||
| ||P1P_1.txt.rev.soap.PE.out||11887236||4051377||34.08|| | | ||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||P2P_1.txt.fwd.soap.PE.out||10570835||3719618||35.19||67.49% | ||
|- | |- | ||
| ||P2P_1.txt.rev.soap.PE.out||10570835||3414342||32.3|| | | ||P2P_1.txt.rev.soap.PE.out||10570835||3414342||32.3|| | ||
|- | |- | ||
| P3P||P3P_1.txt.fwd.soap.PE.out||12343982||4467880||36.19||69.43 | | 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|| | | ||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||P4P_1.txt.fwd.soap.PE.out||13306437||4612404||34.66||66.16% | ||
|- | |- | ||
| ||P4P_1.txt.rev.soap.PE.out||13306437||4191194||31.5|| | | ||P4P_1.txt.rev.soap.PE.out||13306437||4191194||31.5|| | ||
|- | |- | ||
| P5P||P5P_1.txt.fwd.soap.PE.out||16356159||6335050||38.73||75.05 | | 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|| | | ||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||P6P_1.txt.fwd.soap.PE.out||12406211||4691026||37.81||72.84% | ||
|- | |- | ||
| ||P6P_1.txt.rev.soap.PE.out||12406211||4345710||35.03|| | | ||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||P7P_1.txt.fwd.soap.PE.out||14361383||5263978||36.65||71.46% | ||
|- | |- | ||
| ||P7P_1.txt.rev.soap.PE.out||14361383||4998621||34.81|| | | ||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||P8P1_1.txt.fwd.soap.PE.out||15686569||6074276||38.72||74.48% | ||
|- | |- | ||
| ||P8P1_1.txt.rev.soap.PE.out||15686569||5608916||35.76|| | | ||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||P8P2_1.txt.fwd.soap.PE.out||13317181||4960421||37.25||72.68% | ||
|- | |- | ||
| ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43|| | | ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43|| | ||
|}<br> | |}<br> |
Revision as of 01:02, 20 March 2011
Data analysis of sequencing library of Parkinson's patient samples from Burnham
- 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 | 71.4% |
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 | 32.3 | ||
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 | 31.5 | ||
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 |