Genome Sequencer FLX+

Whole Genome Sequencing

Project Information

Client

C1383 - SV912148

Patrick Delahunty

Medicinal Genomics

Sample Information

SID / Sample / Sample Type
18052 / 1 (rec'd 27JUNE11) / Genomic DNA

Quote

SW0001MEDG0511

Deliverable

  1. 454 will prepare one library for the customer supplied plant sample.
  2. 454 will sequence this library in 12 runs using the GS FLX+ chemistry. Typical yield is 900,000 to 1.3 million reads per run, however actual yield may vary.PLEASE NOTE:Customer would like 454 to provide run QC information demonstrating performace of the library.
  3. 454 will assemble the resulting data set using the latest released version of the GS Assembler software.PLEASE NOTE: Customer would like to receive initial assembly results following the completion of 6 runs in order to assess the need for the 6 additional sequencing runs.
  4. 454 will provide all quality filtered reads and associated quality scores in FASTA format along with assembly results.

Delivery Date

August 04, 2011

Sequencing Results

Run Name

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052

D_2011_07_13_10_43_02_frontend2_fullProcessing (2.6)

Run Statistics

Region / SID / Sample / HQ Reads / HQ Bases / Avg Read Length / Mode Read Length / %Mixed / %Dots
1 / 18052 / 1 (rec'd 27JUNE11) / 572,490 / 250,405,061 / 437 / 499 / 11.79% / 5.00%
2 / 18052 / 1 (rec'd 27JUNE11) / 583,048 / 251,961,932 / 432 / 498 / 10.22% / 4.97%

Table 1.0 - Summary of run metrics %Mixed displays the percentage of reads filtered out by the mixed filter, where a mixed read is the result of simultaneously sequencing a mixture of different DNA molecules. %Dots shows the percentage of reads filtered by the dots filter. A dot is an instance of 3 successive nucleotide flows that record no incorporation.

Read Length Distribution

Figure 1.0 - Read length distribution of high quality reads. R1 = 1 (rec'd 27JUNE11), R2 = 1 (rec'd 27JUNE11).

Run Name

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052

D_2011_07_15_14_47_02_frontend2_fullProcessing (2.6)

Run Statistics

Region / SID / Sample / HQ Reads / HQ Bases / Avg Read Length / Mode Read Length / %Mixed / %Dots
1 / 18052 / 1 (rec'd 27JUNE11) / 546,677 / 253,139,632 / 463 / 582 / 15.60% / 4.82%
2 / 18052 / 1 (rec'd 27JUNE11) / 578,882 / 238,515,762 / 412 / 480 / 16.26% / 4.19%

Table 2.0 - Summary of run metrics %Mixed displays the percentage of reads filtered out by the mixed filter, where a mixed read is the result of simultaneously sequencing a mixture of different DNA molecules. %Dots shows the percentage of reads filtered by the dots filter. A dot is an instance of 3 successive nucleotide flows that record no incorporation.

Read Length Distribution

Figure 2.0 - Read length distribution of high quality reads. R1 = 1 (rec'd 27JUNE11), R2 = 1 (rec'd 27JUNE11).

Run Name

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052

D_2011_07_15_14_46_02_frontend2_fullProcessing (2.6)

Run Statistics

Region / SID / Sample / HQ Reads / HQ Bases / Avg Read Length / Mode Read Length / %Mixed / %Dots
1 / 18052 / 1 (rec'd 27JUNE11) / 616,823 / 298,371,650 / 484 / 575 / 11.92% / 4.00%
2 / 18052 / 1 (rec'd 27JUNE11) / 643,310 / 306,828,833 / 477 / 559 / 11.55% / 3.77%

Table 3.0 - Summary of run metrics %Mixed displays the percentage of reads filtered out by the mixed filter, where a mixed read is the result of simultaneously sequencing a mixture of different DNA molecules. %Dots shows the percentage of reads filtered by the dots filter. A dot is an instance of 3 successive nucleotide flows that record no incorporation.

Read Length Distribution

Figure 3.0 - Read length distribution of high quality reads. R1 = 1 (rec'd 27JUNE11), R2 = 1 (rec'd 27JUNE11).

Run Name

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052

D_2011_07_16_13_06_02_frontend2_fullProcessing (2.6)

Run Statistics

Region / SID / Sample / HQ Reads / HQ Bases / Avg Read Length / Mode Read Length / %Mixed / %Dots
1 / 18052 / 1 (rec'd 27JUNE11) / 524,003 / 200,466,632 / 383 / 438 / 16.45% / 5.24%
2 / 18052 / 1 (rec'd 27JUNE11) / 493,012 / 187,654,288 / 381 / 439 / 18.36% / 6.59%

Table 4.0 - Summary of run metrics %Mixed displays the percentage of reads filtered out by the mixed filter, where a mixed read is the result of simultaneously sequencing a mixture of different DNA molecules. %Dots shows the percentage of reads filtered by the dots filter. A dot is an instance of 3 successive nucleotide flows that record no incorporation.

Read Length Distribution

Figure 4.0 - Read length distribution of high quality reads. R1 =1 (rec'd 27JUNE11) , R2 = 1 (rec'd 27JUNE11).

Data Package

The following data files are provided as the delivered product and are available for download at the Roche sFTP site. Please use sftp to obtain the files using a Unix/Linux server. Be sure to type 'bin' to specify binary mode before you 'get' the file. (Alternatively, you can use a browser from Windows or Mac)

User Name: X

Password: X

Server: X

The files are compressed and packaged in .tgz format in Linux, and uploaded to the sFTP server. After downloading (make sure binary file format is specified during download), the .tgz file can be unpacked on a Linux/unix machine by using the command:

tar zxvf samplefile.tgz

The archive can also be unpacked by WinZip or WinRar programs on the Windows platform. However, it is recommended that the customer use a Linux/Unix based operating system to manipulate the files since the volume of data provided is usually much larger than can be comfortably opened and viewed using Microsoft Word or Excel.

File contents: (files shown are after unpacking with tar)

R20110712sc21_sffread.tgz

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/sff/

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/sff/G5T4LHD02.sff

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/sff/G5T4LHD01.sff

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/reads/

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/reads/1.454Reads.fna

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/reads/2.454Reads.qual

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/reads/2.454Reads.fna

R_2011_07_12_09_28_19_sc21_kontoudp_400_7075_93839220_SV912148_18052/D_2011_07_13_10_43_02_frontend2_fullProcessing/reads/1.454Reads.qual

R20110714build09_sffread.tgz

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/sff/

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/sff/G5YGYAB02.sff

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/sff/G5YGYAB01.sff

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/reads/

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/reads/1.454Reads.fna

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/reads/1.454Reads.qual

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/reads/2.454Reads.qual

R_2011_07_14_17_45_36_build09_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_47_02_frontend2_fullProcessing/reads/2.454Reads.fna

R20110714sc20_sffread.tgz

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/sff/

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/sff/G5YGYJV01.sff

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/sff/G5YGYJV02.sff

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/reads/

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/reads/1.454Reads.fna

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/reads/1.454Reads.qual

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/reads/2.454Reads.fna

R_2011_07_14_17_45_45_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_15_14_46_02_frontend2_fullProcessing/reads/2.454Reads.qual

R20110715sc20_sffread.tgz

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/sff/

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/sff/G5Z66BW02.sff

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/sff/G5Z66BW01.sff

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/reads/

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/reads/1.454Reads.fna

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/reads/1.454Reads.qual

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/reads/2.454Reads.fna

R_2011_07_15_16_09_37_sc20_kontoudp_400_7075_93821020_SV912148_18052/D_2011_07_16_13_06_02_frontend2_fullProcessing/reads/2.454Reads.qual

The following is a description of all the files listed above

File Name / Description
region.454Reads.fna / FASTA file of the individual sequence reads.
region.454Reads.qual / Corresponding quality score values for each base in the sequence reads.
sfffilename.sff / Sequence Flowgram Format (SFF) file that represent all quality filtered sequences. It contains information on 454 flowgram signals, basecalls and quality scores and can be used to compile a package suitable for submission to the NCBI trace archive. A description of the SFF format can be found at NCBI at

For Life Science Research use only. Not for diagnostic purposes