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