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| Line 57: | Line 57: | ||
bowtie 1490 1.5% | bowtie 1490 1.5% | ||
* FC638TR_00[12]_8_[12] : 100K reads | * FC638TR_00[12]_8_[12] : 4*100K reads | ||
ref qry aligner #hits %hits | ref qry aligner #hits %hits | ||
cBAC FC638TR_001_8_1 bwasw 42971 43 | cBAC FC638TR_001_8_1 bwasw 42971 43 | ||
Revision as of 21:32, 29 June 2011
Links
Data
- IPST ftp
ftp genomepc1.umd.edu ftpuser pinegenome cd PineUpload052911/ bin mget ...
- cChloroplast
len 120481 gc% 38.55
- cBAC stats
. 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
readLen #mates FC638TR_001_8 146 22,729,231 FC638TR_002_8 146 18,412,638
- Local data
ginkgo: /scratch1/dpuiu/PINE/ /scratch1/dpuiu/PINE/sample/ # 100K mates sampled from each lib /scratch1/dpuiu/PINE/sample/*stats
- Notes:
- First 2bp of each read have higher A count
- GC% variation:
medianGC% cChloroplast 38.55 cBAC 37.61 reads 39.04
Sampled data
- 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