################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634492 Genus_species: Arthrobacter sp. FB24 Taxid: 1663 Genome size: 2400 Libraries: AIAZ, AOWA, AIAY, AIAX ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634492 ------------------------------------------------------------------- ID=3634492 Lineage for 'Arthrobacter sp.': Arthrobacter sp. species Arthrobacter genus Micrococcaceae family Micrococcineae suborder Actinomycetales order Actinobacteridae subclass Actinobacteria (class) class Actinobacteria phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 4880454 # phrap: 4604642 # db: 2400000 3961698 +/- 1110013 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AIAX.5-64 213 95.08 685.93 AIAY.5-44 20 87.64 586.10 AIAZ.5-20 36 78.10 440.08 AOWA.5-44 325 97.57 711.68 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AOWA 325 163 97.58 717.15 162 97.56 706.17 AIAZ 36 16 92.78 530.19 20 66.36 368.00 AIAY 20 10 87.89 597.80 10 87.40 574.40 AIAX 213 106 95.01 682.02 107 95.15 689.81 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634492_fasta.screen -new_ace -minmatch 30 -maxmatch 55 -minscore 55 -revise_greedy -max_subclone_size 50000 -vector_bound 20 > phrap.out /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634492_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634492.out /home/copeland/scripts/librariesInfoTxt.sh 3634492 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634492_fasta.screen -new_ace -minmatch 30 -maxmatch 55 -minscore 55 -revise_greedy -max_subclone_size 50000 -vector_bound 20 > phrap.out /usr/local/src/assembly/pphrap/pxm.SUN3.06OS7 3634492_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634492.out /home/copeland/scripts/librariesInfoTxt.sh 3634492 phrap.out > librariesInfo.txt ################################################################### Library vector screening AIAX.000001.000100 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAX.000101.000200 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAX.000201.000300 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAY.000001.000100 screen.out.1 3634492_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634492_fasta.screen /sequences/LRS.fasta AIAZ.000001.000100 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AOWA.000001.000100 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AOWA.000101.000200 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAX.000001.000100 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAX.000101.000200 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAX.000201.000300 screen.out.1 3634492_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AIAY.000001.000100 screen.out.1 3634492_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634492_fasta.screen /sequences/LRS.fasta AIAZ.000001.000100 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AOWA.000001.000100 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta AOWA.000101.000200 screen.out.1 3634492_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634492_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634492_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 32841 total values totalling 18985808.0000. <578.112969 +/- 179.245711> #Range: [ - 882 ] #Most likely bin: [ 650 - 700 ] 5747 counts #Median bin: [ 600 - 650 ] 4733 counts |XXXX 0 - 50 : [ 554 0.02 0.02 ] |XXXX 50 - 100 : [ 512 0.02 0.03 ] |XXX 100 - 150 : [ 406 0.01 0.04 ] |XXX 150 - 200 : [ 479 0.01 0.06 ] |XXXX 200 - 250 : [ 538 0.02 0.08 ] |XXXXX 250 - 300 : [ 749 0.02 0.10 ] |XXXXXX 300 - 350 : [ 802 0.02 0.12 ] |XXXXXXX 350 - 400 : [ 973 0.03 0.15 ] |XXXXXXXXX 400 - 450 : [ 1228 0.04 0.19 ] |XXXXXXXXXXX 450 - 500 : [ 1634 0.05 0.24 ] |XXXXXXXXXXXXXXXX 500 - 550 : [ 2306 0.07 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3433 0.10 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4733 0.14 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5747 0.17 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5318 0.16 0.90 ] |XXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2826 0.09 0.98 ] |XXXX 800 - 850 : [ 581 0.02 1.00 ] | 850 - 900 : [ 22 0.00 1.00 ] JAZZ trim 15 readlength histogram for AOWA Command: /usr/xpg4/bin/grep AOWA 3634492_fasta.screen.screen.ids > reads.trim15.AOWA.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AOWA.rl 2 50 #Found 7387 total values totalling 4029159.0000. <545.439150 +/- 166.565694> #Range: [ 22 - 824 ] #Most likely bin: [ 600 - 650 ] 1290 counts #Median bin: [ 550 - 600 ] 1040 counts |XX 0 - 50 : [ 64 0.01 0.01 ] |XXXX 50 - 100 : [ 122 0.02 0.03 ] |XXXX 100 - 150 : [ 120 0.02 0.04 ] |XXXX 150 - 200 : [ 127 0.02 0.06 ] |XXXXX 200 - 250 : [ 159 0.02 0.08 ] |XXXXXX 250 - 300 : [ 187 0.03 0.11 ] |XXXXXXX 300 - 350 : [ 233 0.03 0.14 ] |XXXXXXXX 350 - 400 : [ 269 0.04 0.17 ] |XXXXXXXXXXX 400 - 450 : [ 362 0.05 0.22 ] |XXXXXXXXXXXXXXX 450 - 500 : [ 478 0.06 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 729 0.10 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 1040 0.14 0.53 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 1290 0.17 0.70 ] |X