Noi/NOTES/2011-3-17: Difference between revisions
Jump to navigation
Jump to search
>Noi No edit summary |
>Noi No edit summary |
||
(10 intermediate revisions by the same user not shown) | |||
Line 36: | Line 36: | ||
| 8||||||||||||5306||P8P2||M||76.311||P21 | | 8||||||||||||5306||P8P2||M||76.311||P21 | ||
|}<br> | |}<br> | ||
= DMR220k mapping by SOAP = | = DMR220k mapping by SOAP (before trimming) = | ||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' | ||
Line 117: | Line 117: | ||
| ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43(%)|| | | ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43(%)|| | ||
|}<br> | |}<br> | ||
= DMR220k mapping by SOAP (after trimming) = | |||
* Dr. Zhang had the comment that the MmeI digestion in N2-adpator protocol only digested 18/20bp off the capturing arms and leaves another 8-10bp of sequences. He found that trimming the 8-10bp sequences from the 5'-ends of the sequencing reads improved the accuracy of the assay. The methylation levels measured from the two DNA strands (the Watson strand and the Crick strand) of the same CpG sites were compared and the correlate coefficient were calculated. (He suggested to see Supp Figure 2a in his 2009 NBT paper)<br><br> | |||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
Line 197: | Line 199: | ||
|- | |- | ||
| ||P8P2_1.txt.trimmed.rev.soap.PE.out||13317181||4841963||36.36(%)|| | | ||P8P2_1.txt.trimmed.rev.soap.PE.out||13317181||4841963||36.36(%)|| | ||
|}<br> | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=10''' | |||
| align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=50''' | |||
| align="center" style="background:#f0f0f0;"|'''#of cycles''' | |||
| align="center" style="background:#f0f0f0;"|'''Ct value''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=10''' | |||
| align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=50''' | |||
|- | |||
| P1P(trimmed)||0.961||||13||11.46||P1P||0.935||0.957 | |||
|- | |||
| P4P(trimmed)||0.960||||13||11.4||P4P||0.934||0.956 | |||
|- | |||
| P1C (trimmed)||0.957||0.980||13||10.84||P1C||0.925||0.953 | |||
|- | |||
| P2P(trimmed)||0.951||||13||11.45||P2P||0.924||0.951 | |||
|- | |||
| P4C(trimmed)||0.947|| ||13||11.25||P4C||0.918||0.947 | |||
|- | |||
| P3P(trimmed)||0.946||||13||11.2||P3P||0.917||0.952 | |||
|- | |||
| P8C(trimmed)||0.941||||14||12.38||P8C||0.912||0.949 | |||
|- | |||
| P2C(trimmed)||0.936||||16||13.15||P2C||0.913||0.947 | |||
|- | |||
| P3C(trimmed)||0.934||||16||13.49||P3C||0.909||0.947 | |||
|- | |||
| P5C(trimmed)||0.927||||16||13.81||P5C||0.900||0.939 | |||
|- | |||
| P8P1(trimmed)||0.917||||17||14.36|||||| | |||
|- | |||
| P6P(trimmed)||0.912||||17||14.52||P6P||0.885||0.927 | |||
|- | |||
| P8P2(trimmed)||0.912||||17||14.46|||||| | |||
|- | |||
| P5P(trimmed)||0.900||||17||14.91||P5P||0.873||0.923 | |||
|- | |||
| P6C(trimmed)||0.889||||17||14.83||P6C||0.860||0.912 | |||
|- | |||
| P7C1(trimmed)||0.866||0.917||17||14.75 | |||
|- | |||
| P7P(trimmed)||0.828||0.896||20||16.42 | |||
|- | |||
| P7C2(trimmed)||0.789||0.882||20||17.73 | |||
|}<br> | |||
[[File:capturing eff effect-2.png| 700px]]<br> | |||
== Histogram plot == | |||
[[File:histogram001.png]] | |||
[[File:histogram002.png]] | |||
[[File:histogram003.png]] | |||
[[File:histogram004.png]] | |||
== DMS rate == | |||
{| {{table}}border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Samples''' | |||
| align="center" style="background:#f0f0f0;"|'''DMS rate''' | |||
|- | |||
| Pair1||3.40% | |||
|- | |||
| Pair2||0.78% | |||
|- | |||
| Pair3||2.20% | |||
|- | |||
| Pair4||7.30% | |||
|- | |||
| Pair5||8.30% | |||
|- | |||
| Pair8-1||3.74% | |||
|- | |||
| Pair8-2||2.17% | |||
|}<br> | |||
[[File:hcorcluster.PNG]] | |||
* Discussion with Dr. Zhang (2011_03_25) | |||
details later...... | |||
* Rate of mapping after merging trimmed reads and use SE mapping | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Fastq file''' | |||
| align="center" style="background:#f0f0f0;"|'''#Mappable reads''' | |||
| align="center" style="background:#f0f0f0;"|'''#Mapped reads''' | |||
| align="center" style="background:#f0f0f0;"|'''Mapping Rate''' | |||
| align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' | |||
|- | |||
| P1C||P1C_merge_trimmed.txt.fwd.soap.out||23174434||10372464||44.76||86.24 | |||
|- | |||
| ||P1C_merge_trimmed.txt.rev.soap.out||23174434||9613416||41.48|| | |||
|- | |||
| P2C||P2C_merge_trimmed.txt.fwd.soap.out||31762866||14121330||44.46||84.96 | |||
|- | |||
| ||P2C_merge_trimmed.txt.rev.soap.out||31762866||12864985||40.5|| | |||
|- | |||
| P3C||P3C_merge_trimmed.txt.fwd.soap.out||22287452||9936569||44.58||86.02 | |||
|- | |||
| ||P3C_merge_trimmed.txt.rev.soap.out||22287452||9234947||41.44|| | |||
|- | |||
| P4C||P4C_merge_trimmed.txt.fwd.soap.out||25699576||11034635||42.94||82.76 | |||
|- | |||
| ||P4C_merge_trimmed.txt.rev.soap.out||25699576||10233236||39.82|| | |||
|- | |||
| P5C||P5C_merge_trimmed.txt.fwd.soap.out||28442244||13010973||45.75||87.79 | |||
|- | |||
| ||P5C_merge_trimmed.txt.rev.soap.out||28442244||11956478||42.04|| | |||
|- | |||
| P8C||P8C_merge_trimmed.txt.fwd.soap.out||22227154||9521201||42.84||82.59 | |||
|- | |||
| ||P8C_merge_trimmed.txt.rev.soap.out||22227154||8836127||39.75|| | |||
|- | |||
| P1P||P1P_merge_trimmed.txt.fwd.soap.out||23774472||10393409||43.72||83.94 | |||
|- | |||
| ||P1P_merge_trimmed.txt.rev.soap.out||23774472||9561766||40.22|| | |||
|- | |||
| P2P||P2P_merge_trimmed.txt.fwd.soap.out||21141670||8980185||42.48||81.82 | |||
|- | |||
| ||P2P_merge_trimmed.txt.rev.soap.out||21141670||8317535||39.34|| | |||
|- | |||
| P3P||P3P_merge_trimmed.txt.fwd.soap.out||24687964||10578294||42.85||82.44 | |||
|- | |||
| ||P3P_merge_trimmed.txt.rev.soap.out||24687964||9772971||39.59|| | |||
|- | |||
| P4P||P4P_merge_trimmed.txt.fwd.soap.out||26612874||11243003||42.25||80.96 | |||
|- | |||
| ||P4P_merge_trimmed.txt.rev.soap.out||26612874||10302628||38.71|| | |||
|- | |||
| P5P||P5P_merge_trimmed.txt.fwd.soap.out||32712318||14537861||44.44||86.29 | |||
|- | |||
| ||P5P_merge_trimmed.txt.rev.soap.out||32712318||13691284||41.85|| | |||
|- | |||
| P8P1||P8P1_merge_trimmed.txt.fwd.soap.out||31373138||13957523||44.49||85.82 | |||
|- | |||
| ||P8P1_merge_trimmed.txt.rev.soap.out||31373138||12967094||41.33|| | |||
|- | |||
| P8P2||P8P2_merge_trimmed.txt.fwd.soap.out||26634362||11565590||43.42||85.32 | |||
|- | |||
| ||P8P2_merge_trimmed.txt.rev.soap.out||26634362||11160054||41.9|| | |||
|}<br> | |||
* Correlation coefficient is pretty much the same | |||
{| {{table}} border =1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''N''' | |||
| align="center" style="background:#f0f0f0;"|'''MinDepth=10''' | |||
|- | |||
| P1P||41598||0.961 | |||
|- | |||
| P4P||49478||0.960 | |||
|- | |||
| P1C||47853||0.954 | |||
|- | |||
| P2P||41806||0.951 | |||
|- | |||
| P4C||49746||0.947 | |||
|- | |||
| P3P||46043||0.946 | |||
|- | |||
| P8C||40076||0.941 | |||
|- | |||
| P2C||42901||0.935 | |||
|- | |||
| P3C||38510||0.934 | |||
|- | |||
| P5C||48785||0.927 | |||
|- | |||
| P8P1||44087||0.917 | |||
|- | |||
| P8P2||46714||0.911 | |||
|- | |||
| P5P||55131||0.900 | |||
|}<br> | |}<br> |
Latest revision as of 09:40, 28 March 2011
Data analysis of sequencing library of Parkinson's patient samples from Burnham Institute[edit]
- Sequencing library ID: NP-220K-Parkinson_Ind1-18-Feb15, HL089 run
- Library construction: [[1]]
Sample information[edit]
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 (before trimming)[edit]
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(%) |
DMR220k mapping by SOAP (after trimming)[edit]
- Dr. Zhang had the comment that the MmeI digestion in N2-adpator protocol only digested 18/20bp off the capturing arms and leaves another 8-10bp of sequences. He found that trimming the 8-10bp sequences from the 5'-ends of the sequencing reads improved the accuracy of the assay. The methylation levels measured from the two DNA strands (the Watson strand and the Crick strand) of the same CpG sites were compared and the correlate coefficient were calculated. (He suggested to see Supp Figure 2a in his 2009 NBT paper)
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(%) |
Sample | Correlation coefficient MinDepth=10 |
Correlation coefficient MinDepth=50 |
#of cycles | Ct value | Sample | Correlation coefficient MinDepth=10 |
Correlation coefficient MinDepth=50 |
P1P(trimmed) | 0.961 | 13 | 11.46 | P1P | 0.935 | 0.957 | |
P4P(trimmed) | 0.960 | 13 | 11.4 | P4P | 0.934 | 0.956 | |
P1C (trimmed) | 0.957 | 0.980 | 13 | 10.84 | P1C | 0.925 | 0.953 |
P2P(trimmed) | 0.951 | 13 | 11.45 | P2P | 0.924 | 0.951 | |
P4C(trimmed) | 0.947 | 13 | 11.25 | P4C | 0.918 | 0.947 | |
P3P(trimmed) | 0.946 | 13 | 11.2 | P3P | 0.917 | 0.952 | |
P8C(trimmed) | 0.941 | 14 | 12.38 | P8C | 0.912 | 0.949 | |
P2C(trimmed) | 0.936 | 16 | 13.15 | P2C | 0.913 | 0.947 | |
P3C(trimmed) | 0.934 | 16 | 13.49 | P3C | 0.909 | 0.947 | |
P5C(trimmed) | 0.927 | 16 | 13.81 | P5C | 0.900 | 0.939 | |
P8P1(trimmed) | 0.917 | 17 | 14.36 | ||||
P6P(trimmed) | 0.912 | 17 | 14.52 | P6P | 0.885 | 0.927 | |
P8P2(trimmed) | 0.912 | 17 | 14.46 | ||||
P5P(trimmed) | 0.900 | 17 | 14.91 | P5P | 0.873 | 0.923 | |
P6C(trimmed) | 0.889 | 17 | 14.83 | P6C | 0.860 | 0.912 | |
P7C1(trimmed) | 0.866 | 0.917 | 17 | 14.75 | |||
P7P(trimmed) | 0.828 | 0.896 | 20 | 16.42 | |||
P7C2(trimmed) | 0.789 | 0.882 | 20 | 17.73 |
File:Capturing eff effect-2.png
Histogram plot[edit]
File:Histogram001.png File:Histogram002.png File:Histogram003.png File:Histogram004.png
DMS rate[edit]
Samples | DMS rate |
Pair1 | 3.40% |
Pair2 | 0.78% |
Pair3 | 2.20% |
Pair4 | 7.30% |
Pair5 | 8.30% |
Pair8-1 | 3.74% |
Pair8-2 | 2.17% |
- Discussion with Dr. Zhang (2011_03_25)
details later......
- Rate of mapping after merging trimmed reads and use SE mapping
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | Combined Mapping Rate |
P1C | P1C_merge_trimmed.txt.fwd.soap.out | 23174434 | 10372464 | 44.76 | 86.24 |
P1C_merge_trimmed.txt.rev.soap.out | 23174434 | 9613416 | 41.48 | ||
P2C | P2C_merge_trimmed.txt.fwd.soap.out | 31762866 | 14121330 | 44.46 | 84.96 |
P2C_merge_trimmed.txt.rev.soap.out | 31762866 | 12864985 | 40.5 | ||
P3C | P3C_merge_trimmed.txt.fwd.soap.out | 22287452 | 9936569 | 44.58 | 86.02 |
P3C_merge_trimmed.txt.rev.soap.out | 22287452 | 9234947 | 41.44 | ||
P4C | P4C_merge_trimmed.txt.fwd.soap.out | 25699576 | 11034635 | 42.94 | 82.76 |
P4C_merge_trimmed.txt.rev.soap.out | 25699576 | 10233236 | 39.82 | ||
P5C | P5C_merge_trimmed.txt.fwd.soap.out | 28442244 | 13010973 | 45.75 | 87.79 |
P5C_merge_trimmed.txt.rev.soap.out | 28442244 | 11956478 | 42.04 | ||
P8C | P8C_merge_trimmed.txt.fwd.soap.out | 22227154 | 9521201 | 42.84 | 82.59 |
P8C_merge_trimmed.txt.rev.soap.out | 22227154 | 8836127 | 39.75 | ||
P1P | P1P_merge_trimmed.txt.fwd.soap.out | 23774472 | 10393409 | 43.72 | 83.94 |
P1P_merge_trimmed.txt.rev.soap.out | 23774472 | 9561766 | 40.22 | ||
P2P | P2P_merge_trimmed.txt.fwd.soap.out | 21141670 | 8980185 | 42.48 | 81.82 |
P2P_merge_trimmed.txt.rev.soap.out | 21141670 | 8317535 | 39.34 | ||
P3P | P3P_merge_trimmed.txt.fwd.soap.out | 24687964 | 10578294 | 42.85 | 82.44 |
P3P_merge_trimmed.txt.rev.soap.out | 24687964 | 9772971 | 39.59 | ||
P4P | P4P_merge_trimmed.txt.fwd.soap.out | 26612874 | 11243003 | 42.25 | 80.96 |
P4P_merge_trimmed.txt.rev.soap.out | 26612874 | 10302628 | 38.71 | ||
P5P | P5P_merge_trimmed.txt.fwd.soap.out | 32712318 | 14537861 | 44.44 | 86.29 |
P5P_merge_trimmed.txt.rev.soap.out | 32712318 | 13691284 | 41.85 | ||
P8P1 | P8P1_merge_trimmed.txt.fwd.soap.out | 31373138 | 13957523 | 44.49 | 85.82 |
P8P1_merge_trimmed.txt.rev.soap.out | 31373138 | 12967094 | 41.33 | ||
P8P2 | P8P2_merge_trimmed.txt.fwd.soap.out | 26634362 | 11565590 | 43.42 | 85.32 |
P8P2_merge_trimmed.txt.rev.soap.out | 26634362 | 11160054 | 41.9 |
- Correlation coefficient is pretty much the same
Sample | N | MinDepth=10 |
P1P | 41598 | 0.961 |
P4P | 49478 | 0.960 |
P1C | 47853 | 0.954 |
P2P | 41806 | 0.951 |
P4C | 49746 | 0.947 |
P3P | 46043 | 0.946 |
P8C | 40076 | 0.941 |
P2C | 42901 | 0.935 |
P3C | 38510 | 0.934 |
P5C | 48785 | 0.927 |
P8P1 | 44087 | 0.917 |
P8P2 | 46714 | 0.911 |
P5P | 55131 | 0.900 |