Pine tree

Links

• dendrome@ucdavis
• pinegenome.org
• NCBI Taxonomy record Pinus taeda or "loblolly pine"

Data

• UCDAVIS plone

 https://dendrome.ucdavis.edu/TGPlone/research-projects/pinerefseq  
 dpuiu
 ddr5fft6 
 https://dendrome.ucdavis.edu/TGPlone/research-projects/pinerefseq/files/library-and-flow-cell-data/prs-tracking-database-archive/

• IPST ftp

 ftp genomepc1.umd.edu
 ftpuser
 pinegenome

 cd PineUpload052911/
 bin
 prompt             # no Y/N?
 mget *

• Local data

 ginkgo:
 /scratch1/dpuiu/PINE/

PineUpload052911

Chloroplast

                len      gc%
 cChloroplast   120481   38.55

cBACs

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 len     102        8288   89909  116121 140549 172161     113400     126689     11566806       
 gc%     102        34.44  36.56  37.61  38.80  52.88      37.94      37.66      3870.87        

Reads

 library        readLen   #mates
 FC638TR_001_8  146       22,729,231
 FC638TR_002_8  146       18,412,638

• Notes
  • First 2bp of each read have higher A count
  • GC% variation:

                medianGC% 
 cChloroplast   38.55
 cBAC           37.61
 reads          39.04

• cCholoplast alignments (bwasw)

 library               #hits   %hits 
 FC638TR_001_8_1	475254	2.09
 FC638TR_001_8_2	473331	2.08
 FC638TR_002_8_1	1009331	5.48
 FC638TR_002_8_2	1004341	5.45

• cBAC alignments (bwasw)

 library               #hits   %hits 
 FC638TR_001_8_1	9722204	42.77
 FC638TR_001_8_2	9481188	41.71
 FC638TR_002_8_1	7684164	41.73
 FC638TR_002_8_2	7469151	40.56

Sampled reads

• 100K sampled reads from each library (2*2*100K=400K)

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 gc%     400000     0.68   34.93  39.04  43.15  95.89      39.20      40.41      .

• FC638TR_001_8_1 : 100K reads

 ref            qry               aligner      #hits      %hits   %identity(median)
 cBAC           FC638TR_001_8_1   bwasw        42971      43 
                                  nucmer       12477      12.5    95
                                  bowtie       1186       1.2%
 cChloroplast                     bwasw        2031       2%
                                  nucmer       1943       1.9%    100
                                  bowtie       1490       1.5%

• FC638TR_00[12]_8_[12] : 4*100K reads

 ref            qry               aligner      #hits      %hits 
 cBAC           FC638TR_001_8_1   bwasw        42971      43
                FC638TR_001_8_2                41915      42
                FC638TR_002_8_1                42128      42
                FC638TR_002_8_2                40606      41

 cChloroplast   FC638TR_001_8_1                2031       2
                FC638TR_001_8_2                2033       2
                FC638TR_002_8_1                5370       5.3
                FC638TR_002_8_2                5330       5.3

1. mates 160,156 readLen

 FC70M6V_6_001            160,156  23546475  
 TIL_242_FC70M6V_2_002    160,156  9917211   
 TIL_242_FC70M6V_3_002    160,156  6276300   
 TIL_254_FC70M6V_2_004    160,156  9279789   
 TIL_254_FC70M6V_3_004    160,156  5924239   
 TIL_270_FC70M6V_2_003    160,156  10188776  
 TIL_270_FC70M6V_3_003    160,156  6556676   
 TIL_288_FC70M6V_2_001    160,156  9524524   
 TIL_288_FC70M6V_3_001    160,156  6158919