################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634504 Genus_species: Deinococcus geothermalis DSM11300 Taxid: 68909 Genome size: 3000 Libraries: AICY, AICZ, AICX ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634504 ------------------------------------------------------------------- ID=3634504 Lineage for 'Deinococcus geothermalis': Deinococcus geothermalis species Deinococcus genus Deinococcaceae family Deinococcales order Deinococci class Deinococcus-Thermus phylum Bacteria superkingdom cellular organisms no rank root no rank ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 3150337 # phrap: 2870349 # db: 3000000 3006895 +/- 114408 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AICX.5-32 168 98.49 759.54 AICY.5-92 194 94.66 701.79 AICZ.5-20 32 98.73 698.78 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AICY 194 97 93.93 699.38 97 95.39 704.20 AICZ 32 16 98.96 711.19 16 98.50 686.38 AICX 168 84 98.82 757.35 84 98.15 761.74 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634504_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 3634504_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634504.out /home/copeland/scripts/librariesInfoTxt.sh 3634504 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634504_fasta.screen -new_ace -view -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 3634504_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634504.out /home/copeland/scripts/librariesInfoTxt.sh 3634504 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634504_fasta.screen -new_ace -view -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 3634504_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634504.out /home/copeland/scripts/librariesInfoTxt.sh 3634504 phrap.out > librariesInfo.txt ################################################################### Library vector screening AICX.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICY.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICY.000101.000200 screen.out.1 3634504_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICZ.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 3634504_fasta.screen /usr/local/sequences/LRS.fasta AICX.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pUC18.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICY.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICY.000101.000200 screen.out.1 3634504_fasta.screen /tmp/pMCL200.fa.4 screen.out.std 3634504_fasta.screen /sequences/LRS.fasta AICZ.000001.000100 screen.out.1 3634504_fasta.screen /tmp/pCC1Fos.fa.4 screen.out.std 3634504_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634504_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 1939 total values totalling 1472602.0000. <759.464673 +/- 128.578142> #Range: [ - 920 ] #Most likely bin: [ 800 - 850 ] 687 counts #Median bin: [ 750 - 800 ] 607 counts | 0 - 50 : [ 6 0.00 0.00 ] | 50 - 100 : [ 4 0.00 0.01 ] | 100 - 150 : [ 5 0.00 0.01 ] |X 150 - 200 : [ 10 0.01 0.01 ] | 200 - 250 : [ 6 0.00 0.02 ] |X 250 - 300 : [ 11 0.01 0.02 ] |X 300 - 350 : [ 13 0.01 0.03 ] |X 350 - 400 : [ 18 0.01 0.04 ] |X 400 - 450 : [ 18 0.01 0.05 ] |X 450 - 500 : [ 23 0.01 0.06 ] |X 500 - 550 : [ 17 0.01 0.07 ] |XX 550 - 600 : [ 26 0.01 0.08 ] |XX 600 - 650 : [ 27 0.01 0.09 ] |XXXXX 650 - 700 : [ 81 0.04 0.14 ] |XXXXXXXXXXX 700 - 750 : [ 193 0.10 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 607 0.31 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 687 0.35 0.90 ] |XXXXXXXXXXX 850 - 900 : [ 184 0.09 1.00 ] | 900 - 950 : [ 3 0.00 1.00 ] JAZZ trim 15 readlength histogram for AICX Command: /usr/xpg4/bin/grep AICX 3634504_fasta.screen.screen.ids > reads.trim15.AICX.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AICX.rl 2 50 #Found 1939 total values totalling 1472602.0000. <759.464673 +/- 128.578142> #Range: [ - 920 ] #Most likely bin: [ 800 - 850 ] 687 counts #Median bin: [ 750 - 800 ] 607 counts | 0 - 50 : [ 6 0.00 0.00 ] | 50 - 100 : [ 4 0.00 0.01 ] | 100 - 150 : [ 5 0.00 0.01 ] |X 150 - 200 : [ 10 0.01 0.01 ] | 200 - 250 : [ 6 0.00 0.02 ] |X 250 - 300 : [ 11 0.01 0.02 ] |X 300 - 350 : [ 13 0.01 0.03 ] |X 350 - 400 : [ 18 0.01 0.04 ] |X 400 - 450 : [ 18 0.01 0.05 ] |X 450 - 500 : [ 23 0.01 0.06 ] |X 500 - 550 : [ 17 0.01 0.07 ] |XX 550 - 600 : [ 26 0.01 0.08 ] |XX 600 - 650 : [ 27 0.01 0.09 ] |XXXXX 650 - 700 : [ 81 0.04 0.14 ] |XXXXXXXXXXX 700 - 750 : [ 193 0.10 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 607 0.31 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 687 0.35 0.90 ] |XXXXXXXXXXX 850 - 900 : [ 184 0.09 1.00 ] | 900 - 950 : [ 3 0.00 1.00 ] JAZZ trim 15 readlength histogram for AICY JAZZ trim 15 readlength histogram for AICZ ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634504_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634504_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 34807 total values totalling 23104.0795. <0.663777 +/- 0.038602> #Range: [ 0.3913 - 0.8824 ] #Most likely bin: [ 0.67 - 0.675 ] 2032 counts #Median bin: [ 0.665 - 0.67 ] 1993 counts | 0.39 - 0.395 : [ 3 0.00 0.00 ] #... | 0.4 - 0.405 : [ 1 0.00 0.00 ] #... | 0.41 - 0.415 : [ 1 0.00 0.00 ] | 0.415 - 0.42 : [ 4 0.00 0.00 ] | 0.42 - 0.425 : [ 4 0.00 0.00 ] | 0.425 - 0.43 : [ 6 0.00 0.00 ] | 0.43 - 0.435 : [ 4 0.00 0.00 ] | 0.435 - 0.44 : [ 4 0.00 0.00 ] | 0.44 - 0.445 : [ 1 0.00 0.00 ] | 0.445 - 0.45 : [ 2 0.00 0.00 ] | 0.45 - 0.455 : [ 3 0.00 0.00 ] | 0.455 - 0.46 : [ 2 0.00 0.00 ] | 0.46 - 0.465 : [ 5 0.00 0.00 ] | 0.465 - 0.47 : [ 3 0.00 0.00 ] | 0.47 - 0.475 : [ 2 0.00 0.00 ] | 0.475 - 0.48 : [ 6 0.00 0.00 ] | 0.48 - 0.485 : [ 11 0.00 0.00 ] | 0.485 - 0.49 : [ 13 0.00 0.00 ] | 0.49 - 0.495 : [ 11 0.00 0.00 ] | 0.495 - 0.5 : [ 13 0.00 0.00 ] | 0.5 - 0.505 : [ 24 0.00 0.00 ] | 0.505 - 0.51 : [ 16 0.00 0.00 ] | 0.51 - 0.515 : [ 25 0.00 0.00 ] | 0.515 - 0.52 : [ 22 0.00 0.01 ] | 0.52 - 0.525 : [ 21 0.00 0.01 ] |X 0.525 - 0.53 : [ 30 0.00 0.01 ] |X 0.53 - 0.535 : [ 29 0.00 0.01 ] |X 0.535 - 0.54 : [ 28 0.00 0.01 ] |X 0.54 - 0.545 : [ 41 0.00 0.01 ] |X 0.545 - 0.55 : [ 31 0.00 0.01 ] |X 0.55 - 0.555 : [ 43 0.00 0.01 ] |X 0.555 - 0.56 : [ 75 0.00 0.01 ] |X 0.56 - 0.565 : [ 67 0.00 0.02 ] |XX 0.565 - 0.57 : [ 108 0.00 0.02 ] |XX 0.57 - 0.575 : [ 125 0.00 0.02 ] |XX 0.575 - 0.58 : [ 122 0.00 0.03 ] |XXX 0.58 - 0.585 : [ 147 0.00 0.03 ] |XXXX 0.585 - 0.59 : [ 187 0.01 0.04 ] |XXXXX 0.59 - 0.595 : [ 238 0.01 0.04 ] |XXXXX 0.595 - 0.6 : [ 276 0.01 0.05 ] |XXXXXXX 0.6 - 0.605 : [ 363 0.01 0.06 ] |XXXXXXXXX 0.605 - 0.61 : [ 442 0.01 0.07 ] |XXXXXXXXXXX 0.61 - 0.615 : [ 550 0.02 0.09 ] |XXXXXXXXXXXXXX 0.615 - 0.62 : [ 690 0.02 0.11 ] |XXXXXXXXXXXXXXXX 0.62 - 0.625 : [ 796 0.02 0.13 ] |XXXXXXXXXXXXXXXXXXXX 0.625 - 0.63 : [ 1018 0.03 0.16 ] |XXXXXXXXXXXXXXXXXXXXXX 0.63 - 0.635 : [ 1103 0.03 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 0.635 - 0.64 : [ 1322 0.04 0.23 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.64 - 0.645 : [ 1526 0.04 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1638 0.05 0.32 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1772 0.05 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 1846 0.05 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 1927 0.06 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 1993 0.06 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 2032 0.06 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 1962 0.06 0.65 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 1874 0.05 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 1728 0.05 0.76 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 1548 0.04 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 1437 0.04 0.84 ] |XXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 1235 0.04 0.88 ] |XXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 1084 0.03 0.91 ] |XXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 839 0.02 0.93 ] |XXXXXXXXXXXXX 0.715 - 0.72 : [ 670 0.02 0.95 ] |XXXXXXXXXX 0.72 - 0.725 : [ 533 0.02 0.97 ] |XXXXXXX 0.725 - 0.73 : [ 335 0.01 0.98 ] |XXXX 0.73 - 0.735 : [ 204 0.01 0.98 ] |XXX 0.735 - 0.74 : [ 172 0.00 0.99 ] |XX 0.74 - 0.745 : [ 118 0.00 0.99 ] |XX 0.745 - 0.75 : [ 94 0.00 0.99 ] |X 0.75 - 0.755 : [ 56 0.00 1.00 ] |X 0.755 - 0.76 : [ 42 0.00 1.00 ] | 0.76 - 0.765 : [ 25 0.00 1.00 ] | 0.765 - 0.77 : [ 23 0.00 1.00 ] | 0.77 - 0.775 : [ 11 0.00 1.00 ] | 0.775 - 0.78 : [ 12 0.00 1.00 ] | 0.78 - 0.785 : [ 11 0.00 1.00 ] | 0.785 - 0.79 : [ 4 0.00 1.00 ] | 0.79 - 0.795 : [ 4 0.00 1.00 ] | 0.795 - 0.8 : [ 2 0.00 1.00 ] | 0.8 - 0.805 : [ 2 0.00 1.00 ] | 0.805 - 0.81 : [ 3 0.00 1.00 ] | 0.81 - 0.815 : [ 2 0.00 1.00 ] | 0.815 - 0.82 : [ 1 0.00 1.00 ] | 0.82 - 0.825 : [ 2 0.00 1.00 ] #... | 0.83 - 0.835 : [ 1 0.00 1.00 ] #... | 0.88 - 0.885 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones LIBRARY @ ] 34919 17493 90.64 cumulative total @@ Only indicates plates present in input file. Make no assumption regarding plates (not) present in project that do not appear above. ################################################################### Reads in assembly summary Small Inserts = 1 HQ Discrepant reads = 39 Chimeric reads = 164 Suspect alignments = 2687 ################################################################### C O N T I G I N F O R M A T I O N Mon Sep 6 02:10:30 2004 File: /psf/project/microbe3/3634504/edit_dir.07Apr04.QD/phrap.out Contig 86. 139 reads; 22692 bp (untrimmed), 22439 (trimmed). Contig 87. 143 reads; 21932 bp (untrimmed), 21368 (trimmed). Contig 88. 170 reads; 30336 bp (untrimmed), 30188 (trimmed). Contig 89. 199 reads; 34649 bp (untrimmed), 34376 (trimmed). Contig 90. 228 reads; 29841 bp (untrimmed), 29802 (trimmed). Contig 91. 236 reads; 36046 bp (untrimmed), 35805 (trimmed). Contig 92. 237 reads; 21339 bp (untrimmed), 21289 (trimmed). Contig 93. 245 reads; 38936 bp (untrimmed), 38928 (trimmed). Contig 94. 270 reads; 30022 bp (untrimmed), 29877 (trimmed). Contig 95. 300 reads; 29308 bp (untrimmed), 29285 (trimmed). Contig 96. 311 reads; 50708 bp (untrimmed), 50688 (trimmed). Contig 97. 341 reads; 32048 bp (untrimmed), 31891 (trimmed). Contig 98. 344 reads; 34052 bp (untrimmed), 34011 (trimmed). Contig 99. 388 reads; 40071 bp (untrimmed), 40051 (trimmed). Contig 100. 499 reads; 70582 bp (untrimmed), 70524 (trimmed). Contig 101. 751 reads; 64298 bp (untrimmed), 64178 (trimmed). Contig 102. 937 reads; 89222 bp (untrimmed), 89202 (trimmed). Contig 103. 992 reads; 72583 bp (untrimmed), 72530 (trimmed). Contig 104. 1390 reads; 110817 bp (untrimmed), 110792 (trimmed). Contig 105. 1520 reads; 117209 bp (untrimmed), 117175 (trimmed). Contig 106. 2102 reads; 158365 bp (untrimmed), 158245 (trimmed). Contig 107. 2628 reads; 175822 bp (untrimmed), 175814 (trimmed). Contig 108. 2794 reads; 228710 bp (untrimmed), 228684 (trimmed). Contig 109. 3478 reads; 278606 bp (untrimmed), 278544 (trimmed). Contig 110. 3697 reads; 289255 bp (untrimmed), 289224 (trimmed). Contig 111. 3973 reads; 317038 bp (untrimmed), 316875 (trimmed). Contig 112. 5049 reads; 421330 bp (untrimmed), 421243 (trimmed). -------------------------------------------------------------- Totals 34860 reads; 3164085 bp (untrimmed), 3150337 (trimmed). ################################################################### Histogram of Good Contig Trimmed Length (>=2000 bp & >=10 reads) ------------------------------------------------------------------- Command: contig | grep '^Contig' | hist - 8 2000 3 10 10000000 8 2000 10000000 Total Good Ctgs: Total Size Good Ctgs: #Found 51 total values totalling 3039954.0000. <59606.941176 +/- 92022.714128> #Range: [ 2345 - 421243 ] #Most likely bin: [ 2000 - 4000 ] 5 counts #Median bin: [ 20000 - 22000 ] 2 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 5 0.10 0.10 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 4 0.08 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 8000 : [ 5 0.10 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXX 8000 - 10000 : [ 3 0.06 0.33 ] |XXXXXXXXXXXXXXXX 10000 - 12000 : [ 2 0.04 0.37 ] |XXXXXXXXXXXXXXXX 12000 - 14000 : [ 2 0.04 0.41 ] |XXXXXXXX 14000 - 16000 : [ 1 0.02 0.43 ] #... |XXXXXXXXXXXXXXXX 18000 - 20000 : [ 2 0.04 0.47 ] |XXXXXXXXXXXXXXXX 20000 - 22000 : [ 2 0.04 0.51 ] |XXXXXXXX 22000 - 24000 : [ 1 0.02 0.53 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 28000 - 30000 : [ 3 0.06 0.59 ] |XXXXXXXXXXXXXXXX 30000 - 32000 : [ 2 0.04 0.63 ] #... |XXXXXXXXXXXXXXXXXXXXXXXX 34000 - 36000 : [ 3 0.06 0.69 ] #... |XXXXXXXX 38000 - 40000 : [ 1 0.02 0.71 ] |XXXXXXXX 40000 - 42000 : [ 1 0.02 0.73 ] #... |XXXXXXXX 50000 - 52000 : [ 1 0.02 0.75 ] #... |XXXXXXXX 64000 - 66000 : [ 1 0.02 0.76 ] #... |XXXXXXXX 70000 - 72000 : [ 1 0.02 0.78 ] |XXXXXXXX 72000 - 74000 : [ 1 0.02 0.80 ] #... |XXXXXXXX 88000 - 90000 : [ 1 0.02 0.82 ] #... |XXXXXXXX 110000 - 112000 : [ 1 0.02 0.84 ] #... |XXXXXXXX 116000 - 118000 : [ 1 0.02 0.86 ] #... |XXXXXXXX 158000 - 160000 : [ 1 0.02 0.88 ] #... |XXXXXXXX 174000 - 176000 : [ 1 0.02 0.90 ] #... |XXXXXXXX 228000 - 230000 : [ 1 0.02 0.92 ] #... |XXXXXXXX 278000 - 280000 : [ 1 0.02 0.94 ] #... |XXXXXXXX 288000 - 290000 : [ 1 0.02 0.96 ] #... |XXXXXXXX 316000 - 318000 : [ 1 0.02 0.98 ] #... |XXXXXXXX 420000 - 422000 : [ 1 0.02 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 5610556 C = 10938887 G = 10928493 T = 5701045 N = 145942 X = 372419 GC fraction = 0.65 Total = 33697342 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634504_fasta.screen.contigs A 527423 C 1051876 G 1049776 N 45 T 534928 X 37 fraction GC = 0.66 total bases = 3164085 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 3046604 bases = 10.44 +- 4.61 = 0.15 +- 3.70 m1 = 2.03 m2 = 1.88 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 51 total values totalling 364.2500. <7.142157 +/- 3.056013> #Range: [ 2.17 - 13.68 ] #Most likely bin: [ 5.5 - 6 ] 6 counts #Median bin: [ 5.5 - 6 ] 6 counts |XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.06 0.06 ] |XXXXXXX 2.5 - 3 : [ 1 0.02 0.08 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.08 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 6 0.12 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.12 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.12 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 4 0.08 0.59 ] |XXXXXXX 6.5 - 7 : [ 1 0.02 0.61 ] |XXXXXXX 7 - 7.5 : [ 1 0.02 0.63 ] #... |XXXXXXXXXXXXX 8 - 8.5 : [ 2 0.04 0.67 ] |XXXXXXX 8.5 - 9 : [ 1 0.02 0.69 ] |XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.04 0.73 ] |XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.76 ] |XXXXXXX 10 - 10.5 : [ 1 0.02 0.78 ] |XXXXXXX 10.5 - 11 : [ 1 0.02 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.08 0.88 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.06 0.94 ] |XXXXXXX 12 - 12.5 : [ 1 0.02 0.96 ] |XXXXXXX 12.5 - 13 : [ 1 0.02 0.98 ] #... |XXXXXXX 13.5 - 14 : [ 1 0.02 1.00 ] Histogram of Major Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000 #Found 51 total values totalling 364.2500. <7.142157 +/- 3.056013> #Range: [ 2.17 - 13.68 ] #Most likely bin: [ 5.5 - 6 ] 6 counts #Median bin: [ 5.5 - 6 ] 6 counts |XXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 3 0.06 0.06 ] |XXXXXXX 2.5 - 3 : [ 1 0.02 0.08 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 4.5 : [ 4 0.08 0.16 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4.5 - 5 : [ 6 0.12 0.27 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 5.5 : [ 6 0.12 0.39 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5.5 - 6 : [ 6 0.12 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 6 - 6.5 : [ 4 0.08 0.59 ] |XXXXXXX 6.5 - 7 : [ 1 0.02 0.61 ] |XXXXXXX 7 - 7.5 : [ 1 0.02 0.63 ] #... |XXXXXXXXXXXXX 8 - 8.5 : [ 2 0.04 0.67 ] |XXXXXXX 8.5 - 9 : [ 1 0.02 0.69 ] |XXXXXXXXXXXXX 9 - 9.5 : [ 2 0.04 0.73 ] |XXXXXXXXXXXXX 9.5 - 10 : [ 2 0.04 0.76 ] |XXXXXXX 10 - 10.5 : [ 1 0.02 0.78 ] |XXXXXXX 10.5 - 11 : [ 1 0.02 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 4 0.08 0.88 ] |XXXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 3 0.06 0.94 ] |XXXXXXX 12 - 12.5 : [ 1 0.02 0.96 ] |XXXXXXX 12.5 - 13 : [ 1 0.02 0.98 ] #... |XXXXXXX 13.5 - 14 : [ 1 0.02 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 95 11 reads 4808 bases = 2.17 +- 0.84 = 0.17 +- 1.19 m1 = 0.32 m2 = -0.18 Contig 99 14 reads 5538 bases = 2.32 +- 1.20 = 0.32 +- 1.47 m1 = 0.62 m2 = -0.18 Contig 101 19 reads 7128 bases = 2.47 +- 1.00 = 0.11 +- 1.56 m1 = 0.40 m2 = -0.36 Contig 96 12 reads 3807 bases = 2.96 +- 1.08 = 1.07 +- 1.53 m1 = 0.39 m2 = -0.29 Contig 108 31 reads 6827 bases = 4.13 +- 2.22 = -0.01 +- 1.77 m1 = 1.19 m2 = 0.45 Contig 106 29 reads 6085 bases = 4.21 +- 2.03 = 1.28 +- 1.78 m1 = 0.98 m2 = 0.23 Contig 107 30 reads 6369 bases = 4.21 +- 1.80 = 0.21 +- 2.81 m1 = 0.77 m2 = -1.16 Contig 97 13 reads 2773 bases = 4.38 +- 1.72 = 1.65 +- 1.47 m1 = 0.67 m2 = 0.20 Contig 104 26 reads 5205 bases = 4.56 +- 2.72 = 0.48 +- 1.94 m1 = 1.62 m2 = 0.90 Contig 110 41 reads 8048 bases = 4.69 +- 1.32 = 0.53 +- 2.09 m1 = 0.37 m2 = -0.65 Contig 111 45 reads 8418 bases = 4.89 +- 2.10 = 0.93 +- 2.72 m1 = 0.90 m2 = -0.74 Contig 102 21 reads 3877 bases = 4.93 +- 2.13 = 1.18 +- 1.54 m1 = 0.92 m2 = 0.53 Contig 116 77 reads 14018 bases = 4.94 +- 2.43 = 0.30 +- 2.61 m1 = 1.19 m2 = -0.23 Contig 120 110 reads 18477 bases = 4.98 +- 1.91 = 0.35 +- 2.39 m1 = 0.73 m2 = -0.51 Contig 112 45 reads 8076 bases = 5.16 +- 1.74 = 0.30 +- 1.75 m1 = 0.59 m2 = -0.01 Contig 103 25 reads 4291 bases = 5.27 +- 1.91 = 0.23 +- 2.46 m1 = 0.69 m2 = -0.60 Contig 124 171 reads 30277 bases = 5.28 +- 2.63 = 0.06 +- 2.37 m1 = 1.31 m2 = 0.33 Contig 119 91 reads 15814 bases = 5.29 +- 2.32 = 0.59 +- 2.38 m1 = 1.01 m2 = -0.07 Contig 125 199 reads 34649 bases = 5.32 +- 2.23 = 0.27 +- 2.37 m1 = 0.93 m2 = -0.16 Contig 98 14 reads 2447 bases = 5.37 +- 2.26 = 4.62 +- 2.35 m1 = 0.95 m2 = -0.10 Contig 126 229 reads 29841 bases = 7.05 +- 2.96 = 0.64 +- 3.28 m1 = 1.25 m2 = -0.49 Contig 118 89 reads 10163 bases = 8.09 +- 3.55 = 1.42 +- 3.92 m1 = 1.56 m2 = -0.70 Contig 130 274 reads 30022 bases = 8.33 +- 3.40 = 0.42 +- 2.76 m1 = 1.39 m2 = 0.99 Contig 135 390 reads 40071 bases = 8.90 +- 3.29 = 0.64 +- 3.28 m1 = 1.22 m2 = 0.02 Contig 134 347 reads 34052 bases = 9.37 +- 3.62 = 0.16 +- 3.38 m1 = 1.40 m2 = 0.42 Contig 131 304 reads 29308 bases = 9.46 +- 3.90 = 0.22 +- 4.11 m1 = 1.61 m2 = -0.42 Contig 138 943 reads 89222 bases = 9.69 +- 3.65 = 0.34 +- 3.30 m1 = 1.37 m2 = 0.61 Contig 133 344 reads 32048 bases = 9.74 +- 4.49 = 0.37 +- 3.09 m1 = 2.07 m2 = 2.65 Contig 128 239 reads 21339 bases = 10.24 +- 4.07 = 0.70 +- 4.13 m1 = 1.62 m2 = -0.12 Contig 137 760 reads 64298 bases = 10.81 +- 4.59 = 0.28 +- 4.09 m1 = 1.95 m2 = 1.09 Contig 148 5083 reads 421330 bases = 11.07 +- 3.97 = 0.08 +- 3.68 m1 = 1.42 m2 = 0.56 Contig 144 2816 reads 228710 bases = 11.27 +- 4.94 = 0.03 +- 3.85 m1 = 2.16 m2 = 2.39 Contig 140 1397 reads 110817 bases = 11.44 +- 3.58 = 0.09 +- 3.49 m1 = 1.12 m2 = 0.17 Contig 145 3507 reads 278606 bases = 11.44 +- 3.77 = -0.01 +- 4.10 m1 = 1.25 m2 = -0.65 Contig 147 4038 reads 317038 bases = 11.69 +- 4.64 = 0.08 +- 4.07 m1 = 1.84 m2 = 1.23 Contig 146 3733 reads 289255 bases = 11.80 +- 3.89 = 0.09 +- 3.92 m1 = 1.28 m2 = -0.05 Contig 141 1536 reads 117208 bases = 11.97 +- 4.22 = -0.09 +- 3.89 m1 = 1.49 m2 = 0.68 Contig 142 2123 reads 158365 bases = 12.21 +- 4.07 = 0.08 +- 4.25 m1 = 1.36 m2 = -0.38 Contig 139 1000 reads 72583 bases = 12.69 +- 4.56 = 0.22 +- 3.96 m1 = 1.64 m2 = 1.28 Contig 143 2649 reads 175822 bases = 13.68 +- 4.39 = 0.06 +- 4.34 m1 = 1.41 m2 = 0.11 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 112 total values totalling 34860.0000. <311.250000 +/- 862.440614> #Range: [ 1 - 5049 ] #Most likely bin: [ 4 - 5 ] 14 counts #Median bin: [ 8 - 9 ] 3 counts |XXXXXX 1 - 2 : [ 2 0.02 0.02 ] #... |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3 - 4 : [ 11 0.10 0.12 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 4 - 5 : [ 14 0.12 0.24 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5 - 6 : [ 12 0.11 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXX 6 - 7 : [ 8 0.07 0.42 ] |XXXXXXXXXXXXXXXXX 7 - 8 : [ 6 0.05 0.47 ] |XXXXXXXXX 8 - 9 : [ 3 0.03 0.50 ] |XXXXXXXXXXX 9 - 10 : [ 4 0.04 0.54 ] |XXX 10 - 11 : [ 1 0.01 0.54 ] #... |XXX 12 - 13 : [ 1 0.01 0.55 ] |XXX 13 - 14 : [ 1 0.01 0.56 ] |XXXXXX 14 - 15 : [ 2 0.02 0.58 ] #... |XXX 18 - 19 : [ 1 0.01 0.59 ] #... |XXX 21 - 22 : [ 1 0.01 0.60 ] #... |XXXXXX 25 - 26 : [ 2 0.02 0.62 ] #... |XXX 28 - 29 : [ 1 0.01 0.62 ] |XXX 29 - 30 : [ 1 0.01 0.63 ] #... |XXX 31 - 32 : [ 1 0.01 0.64 ] #... |XXX 39 - 40 : [ 1 0.01 0.65 ] #... |XXX 41 - 42 : [ 1 0.01 0.66 ] #... |XXX 44 - 45 : [ 1 0.01 0.67 ] |XXX 45 - 46 : [ 1 0.01 0.68 ] #... |XXX 47 - 48 : [ 1 0.01 0.69 ] #... |XXX 59 - 60 : [ 1 0.01 0.70 ] #... |XXX 68 - 69 : [ 1 0.01 0.71 ] #... |XXX 84 - 85 : [ 1 0.01 0.71 ] #... |XXX 89 - 90 : [ 1 0.01 0.72 ] |XXX 90 - 91 : [ 1 0.01 0.73 ] #... |XXX 109 - 110 : [ 1 0.01 0.74 ] #... |XXX 120 - 121 : [ 1 0.01 0.75 ] #... |XXX 123 - 124 : [ 1 0.01 0.76 ] #... |XXX 139 - 140 : [ 1 0.01 0.77 ] #... |XXX 143 - 144 : [ 1 0.01 0.78 ] #... |XXX 170 - 171 : [ 1 0.01 0.79 ] #... |XXX 199 - 200 : [ 1 0.01 0.79 ] #... |XXX 228 - 229 : [ 1 0.01 0.80 ] #... |XXX 236 - 237 : [ 1 0.01 0.81 ] |XXX 237 - 238 : [ 1 0.01 0.82 ] #... |XXX 245 - 246 : [ 1 0.01 0.83 ] #... |XXX 270 - 271 : [ 1 0.01 0.84 ] #... |XXX 300 - 301 : [ 1 0.01 0.85 ] #... |XXX 311 - 312 : [ 1 0.01 0.86 ] #... |XXX 341 - 342 : [ 1 0.01 0.87 ] #... |XXX 344 - 345 : [ 1 0.01 0.88 ] #... |XXX 388 - 389 : [ 1 0.01 0.88 ] #... |XXX 499 - 500 : [ 1 0.01 0.89 ] #... |XXX 751 - 752 : [ 1 0.01 0.90 ] #... |XXX 937 - 938 : [ 1 0.01 0.91 ] #... |XXX 992 - 993 : [ 1 0.01 0.92 ] #... |XXX 1390 - 1391 : [ 1 0.01 0.93 ] #... |XXX 1520 - 1521 : [ 1 0.01 0.94 ] #... |XXX 2102 - 2103 : [ 1 0.01 0.95 ] #... |XXX 2628 - 2629 : [ 1 0.01 0.96 ] #... |XXX 2794 - 2795 : [ 1 0.01 0.96 ] #... |XXX 3478 - 3479 : [ 1 0.01 0.97 ] #... |XXX 3697 - 3698 : [ 1 0.01 0.98 ] #... |XXX 3973 - 3974 : [ 1 0.01 0.99 ] #... |XXX 5049 - 5050 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 112 total values totalling 3164085.0000. <28250.758929 +/- 68428.842116> #Range: [ 230 - 421330 ] #Most likely bin: [ 1000 - 2000 ] 28 counts #Median bin: [ 2000 - 3000 ] 26 counts |XXXXXXXXX 0 - 1000 : [ 6 0.05 0.05 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 28 0.25 0.30 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 3000 : [ 26 0.23 0.54 ] |XXXXXX 3000 - 4000 : [ 4 0.04 0.57 ] |XXXX 4000 - 5000 : [ 3 0.03 0.60 ] |XXX 5000 - 6000 : [ 2 0.02 0.62 ] |XXXXXX 6000 - 7000 : [ 4 0.04 0.65 ] |X 7000 - 8000 : [ 1 0.01 0.66 ] |XXXX 8000 - 9000 : [ 3 0.03 0.69 ] |X 9000 - 10000 : [ 1 0.01 0.70 ] |X 10000 - 11000 : [ 1 0.01 0.71 ] |X 11000 - 12000 : [ 1 0.01 0.71 ] |X 12000 - 13000 : [ 1 0.01 0.72 ] #... |X 14000 - 15000 : [ 1 0.01 0.73 ] |X 15000 - 16000 : [ 1 0.01 0.74 ] #... |X 18000 - 19000 : [ 1 0.01 0.75 ] |X 19000 - 20000 : [ 1 0.01 0.76 ] #... |XXX 21000 - 22000 : [ 2 0.02 0.78 ] |X 22000 - 23000 : [ 1 0.01 0.79 ] #... |XXX 29000 - 30000 : [ 2 0.02 0.80 ] |XXX 30000 - 31000 : [ 2 0.02 0.82 ] #... |X 32000 - 33000 : [ 1 0.01 0.83 ] #... |XXX 34000 - 35000 : [ 2 0.02 0.85 ] #... |X 36000 - 37000 : [ 1 0.01 0.86 ] #... |X 38000 - 39000 : [ 1 0.01 0.87 ] #... |X 40000 - 41000 : [ 1 0.01 0.88 ] #... |X 50000 - 51000 : [ 1 0.01 0.88 ] #... |X 64000 - 65000 : [ 1 0.01 0.89 ] #... |X 70000 - 71000 : [ 1 0.01 0.90 ] #... |X 72000 - 73000 : [ 1 0.01 0.91 ] #... |X 89000 - 90000 : [ 1 0.01 0.92 ] #... |X 110000 - 111000 : [ 1 0.01 0.93 ] #... |X 117000 - 118000 : [ 1 0.01 0.94 ] #... |X 158000 - 159000 : [ 1 0.01 0.95 ] #... |X 175000 - 176000 : [ 1 0.01 0.96 ] #... |X 228000 - 229000 : [ 1 0.01 0.96 ] #... |X 278000 - 279000 : [ 1 0.01 0.97 ] #... |X 289000 - 290000 : [ 1 0.01 0.98 ] #... |X 317000 - 318000 : [ 1 0.01 0.99 ] #... |X 421000 - 422000 : [ 1 0.01 1.00 ] ################################################################### Histogram of Assembled Average Insert Sizes Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list ------------------------------------------------------------------- Command: /usr/xpg4/bin/grep AICX reads.list > grep.reads.list.AICX Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICX 4 500 #Found 7070 total values totalling 26027449.0000. <3681.393069 +/- 2540.400713> #Range: [ - 164214 ] #Most likely bin: [ 3000 - 3500 ] 2646 counts #Median bin: [ 3500 - 4000 ] 2550 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 2 0.00 0.00 ] | 1000 - 1500 : [ 20 0.00 0.00 ] | 1500 - 2000 : [ 19 0.00 0.01 ] |X 2000 - 2500 : [ 59 0.01 0.01 ] |XXX 2500 - 3000 : [ 188 0.03 0.04 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 2646 0.37 0.42 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 2550 0.36 0.78 ] |XXXXXXXXXXXXXXXXXXXXXX 4000 - 4500 : [ 1430 0.20 0.98 ] |XX 4500 - 5000 : [ 150 0.02 1.00 ] | 5000 - 5500 : [ 1 0.00 1.00 ] #... | 30000 - 30500 : [ 1 0.00 1.00 ] #... | 44500 - 45000 : [ 1 0.00 1.00 ] #... | 129500 - 130000 : [ 1 0.00 1.00 ] #... | 164000 - 164500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AICY reads.list > grep.reads.list.AICY Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICY 4 500 #Found 5395 total values totalling 38046278.0000. <7052.136793 +/- 10048.227334> #Range: [ - 364883 ] #Most likely bin: [ 6000 - 6500 ] 1270 counts #Median bin: [ 6500 - 7000 ] 1170 counts | 0 - 500 : [ 1 0.00 0.00 ] #... | 1000 - 1500 : [ 7 0.00 0.00 ] | 1500 - 2000 : [ 8 0.00 0.00 ] | 2000 - 2500 : [ 12 0.00 0.01 ] |X 2500 - 3000 : [ 20 0.00 0.01 ] |X 3000 - 3500 : [ 18 0.00 0.01 ] |X 3500 - 4000 : [ 20 0.00 0.02 ] |X 4000 - 4500 : [ 29 0.01 0.02 ] |X 4500 - 5000 : [ 37 0.01 0.03 ] |XXXXXXXXX 5000 - 5500 : [ 297 0.06 0.08 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 5500 - 6000 : [ 955 0.18 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 1270 0.24 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 1170 0.22 0.71 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 870 0.16 0.87 ] |XXXXXXXXXXXXXXX 7500 - 8000 : [ 484 0.09 0.96 ] |XXXXX 8000 - 8500 : [ 157 0.03 0.99 ] | 8500 - 9000 : [ 2 0.00 0.99 ] | 9000 - 9500 : [ 4 0.00 0.99 ] #... | 11000 - 11500 : [ 2 0.00 0.99 ] | 11500 - 12000 : [ 1 0.00 0.99 ] #... | 12500 - 13000 : [ 1 0.00 0.99 ] #... | 14000 - 14500 : [ 1 0.00 0.99 ] #... | 15000 - 15500 : [ 2 0.00 0.99 ] #... | 23000 - 23500 : [ 1 0.00 1.00 ] #... | 28500 - 29000 : [ 2 0.00 1.00 ] #... | 30500 - 31000 : [ 2 0.00 1.00 ] #... | 35000 - 35500 : [ 1 0.00 1.00 ] #... | 42000 - 42500 : [ 1 0.00 1.00 ] #... | 52000 - 52500 : [ 1 0.00 1.00 ] #... | 64000 - 64500 : [ 1 0.00 1.00 ] #... | 65500 - 66000 : [ 1 0.00 1.00 ] #... | 70000 - 70500 : [ 1 0.00 1.00 ] #... | 73000 - 73500 : [ 1 0.00 1.00 ] #... | 82000 - 82500 : [ 1 0.00 1.00 ] #... | 84000 - 84500 : [ 2 0.00 1.00 ] #... | 99500 - 100000 : [ 1 0.00 1.00 ] #... | 124000 - 124500 : [ 1 0.00 1.00 ] #... | 133500 - 134000 : [ 1 0.00 1.00 ] #... | 140500 - 141000 : [ 1 0.00 1.00 ] #... | 144500 - 145000 : [ 1 0.00 1.00 ] #... | 162000 - 162500 : [ 1 0.00 1.00 ] #... | 179500 - 180000 : [ 1 0.00 1.00 ] #... | 203000 - 203500 : [ 1 0.00 1.00 ] #... | 208500 - 209000 : [ 1 0.00 1.00 ] #... | 232500 - 233000 : [ 1 0.00 1.00 ] #... | 341500 - 342000 : [ 1 0.00 1.00 ] #... | 364500 - 365000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AICZ reads.list > grep.reads.list.AICZ Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AICZ 4 500 #Found 806 total values totalling 31527311.0000. <39115.770471 +/- 3418.664867> #Range: [ - 55017 ] #Most likely bin: [ 39000 - 39500 ] 61 counts #Median bin: [ 39000 - 39500 ] 61 counts |X 0 - 500 : [ 1 0.00 0.00 ] #... |X 29000 - 29500 : [ 2 0.00 0.00 ] #... |X 30000 - 30500 : [ 1 0.00 0.00 ] |X 30500 - 31000 : [ 1 0.00 0.01 ] |X 31000 - 31500 : [ 1 0.00 0.01 ] |XXX 31500 - 32000 : [ 4 0.00 0.01 ] |XXXX 32000 - 32500 : [ 6 0.01 0.02 ] |XXX 32500 - 33000 : [ 5 0.01 0.03 ] |XXXX 33000 - 33500 : [ 6 0.01 0.03 ] |XXXXXXXX 33500 - 34000 : [ 12 0.01 0.05 ] |XXXXXXXXXXXXX 34000 - 34500 : [ 20 0.02 0.07 ] |XXXXXXXXXX 34500 - 35000 : [ 15 0.02 0.09 ] |XXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 27 0.03 0.13 ] |XXXXXXXXXXXXXXX 35500 - 36000 : [ 23 0.03 0.15 ] |XXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 30 0.04 0.19 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 47 0.06 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 48 0.06 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 45 0.06 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 36 0.04 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 55 0.07 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 61 0.08 0.55 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 42 0.05 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 50 0.06 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 41 0.05 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 39 0.05 0.77 ] |XXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 28 0.03 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 39 0.05 0.85 ] |XXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 30 0.04 0.89 ] |XXXXXXXXXX 43000 - 43500 : [ 16 0.02 0.91 ] |XXXXXXXXXXXXXX 43500 - 44000 : [ 22 0.03 0.93 ] |XXXXXXXXXXXXX 44000 - 44500 : [ 20 0.02 0.96 ] |XXXXXXXXX 44500 - 45000 : [ 13 0.02 0.98 ] |XXXXXXX 45000 - 45500 : [ 10 0.01 0.99 ] |XXXXX 45500 - 46000 : [ 7 0.01 1.00 ] |X 46000 - 46500 : [ 1 0.00 1.00 ] #... |X 47000 - 47500 : [ 1 0.00 1.00 ] #... |X 55000 - 55500 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AICY 6451 +- 1135 (n=2766) # AICZ 39039 +- 3052 (n=397) # AICX 3560 +- 961 (n=3550) ################################################################### N50 Calculations: * N50 Contig Reads * Total Assemb Reads: 1/2 (Tot. Assemb Reads): Command: hist contig.grep 3 10 3 (10) (100) Result: Half the total assembled reads are in n of largest contigs containing at least n reads each. ------------------------------------------------------------------- ################################################################### Ideal Assembly with avg read len of 759.464673 bp, 34860 reads, genome size 3006895 bp Command: idealAssembly 3006895 34860 759.464673 ------------------------------------------------------------------- Genome = 3006895 bases Nreads = 34860 readLength = 759.464673 Depth = 8.80 N_contigs = N_gaps = 5 mean gap size = 85 bases mean contig size = 6666 reads (~ 574966 bases) %cover = 99.98 %singlet = 0.00 assembly size = 3006443 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 1 contigs containing at least 11185 reads each * N50 Contig Sizes * Total Assemb Size: 1/2 (Tot.Assemb. Size): Command: hist contig.grep 5 1000 5 (2200) (15000) Result: Half of the total Assembled Size of the genome is contained in n of the largest contigs equaling n bps. ################################################################### Bad M1 Contigs------------------------------------------------------------------- ################################################################### Bad M2 Contigs ------------------------------------------------------------------- ################################################################### Ran Plates2contigs: Output Location: Ran in.dir: Output Location: Viewed Contigs with Phrapview: ################################################################### Conclusions: