################################################################### Phrap Assembly QC Date: 09-08-2004 Project_id: 3634482 Genus_species: Frankia CcI3 Taxid: 106370 Genome size: 8000 Libraries: AHZH, APZK, APZI, AHZG, AHZF ################################################################### Taxonomy summary Command: /home/copeland/scripts/tax2tree.sh 3634482 ------------------------------------------------------------------- ID=3634482 ################################################################### Genome size estimates ------------------------------------------------------------------- # contigs: 5431277 # phrap: 5217047 # db: 8000000 6216108 +/- 1264430 ################################################################### Library/Plate summary ------------------------------------------------------------------- Number of plates run: #runs Pass Rate Average Read Length AHZF.5-56 400 97.94 680.63 AHZG.5-32 316 90.98 552.52 AHZH.5-40 73 84.32 500.85 ################################################################### Run information ------------------------------------------------------------------- Library #Runs #FW Pass Q20s #RV Pass Q20s AHZH 73 36 86.66 521.08 37 82.04 481.16 APZK 0 0 0.00 0.00 0 0.00 0.00 APZI 0 0 0.00 0.00 0 0.00 0.00 AHZG 316 158 91.26 558.93 158 90.71 546.11 AHZF 400 200 97.86 675.53 200 98.02 685.74 ################################################################### Assembly parameters /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634482_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 3634482_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634482.out /home/copeland/scripts/librariesInfoTxt.sh 3634482 phrap.out > librariesInfo.txt /usr/local/src/assembly/pphrap/pphrap.SUN3.57 3634482_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 3634482_fasta.screen.contigs /usr/local/sequences/repeats.seq -minmatch 24 -minscore 40 > alu.screen.out perl /home/copeland/scripts/asseminfo phrap.out > asseminfo.3634482.out /home/copeland/scripts/librariesInfoTxt.sh 3634482 phrap.out > librariesInfo.txt ################################################################### Library vector screening AHZF.000001.000100 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZF.000101.000200 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZF.000201.000300 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000001.000100 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000101.000200 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000201.000300 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZH.000001.000100 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZF.000001.000100 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZF.000101.000200 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZF.000201.000300 screen.out.1 3634482_fasta.screen /usr/local/sequences/production/vectors/pUC18.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000001.000100 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000101.000200 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZG.000201.000300 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pMCL200.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta AHZH.000001.000100 screen.out.1 3634482_fasta.screen /sequences/production/vectors/pCC1Fos.fa screen.out.std 3634482_fasta.screen /usr/local/sequences/LRS.fasta ################################################################### JAZZ trim 15 readlength histogram Command: /home/copeland/scripts/histogram2.pl 3634482_fasta.screen.screen.ids 2 50 ------------------------------------------------------------------- #Found 82635 total values totalling 50592136.0000. <612.236171 +/- 197.199802> #Range: [ 22 - 937 ] #Most likely bin: [ 750 - 800 ] 13506 counts #Median bin: [ 650 - 700 ] 10080 counts |X 0 - 50 : [ 262 0.00 0.00 ] |XXXX 50 - 100 : [ 1253 0.02 0.02 ] |XXXXX 100 - 150 : [ 1610 0.02 0.04 ] |XXXXX 150 - 200 : [ 1644 0.02 0.06 ] |XXXXX 200 - 250 : [ 1839 0.02 0.08 ] |XXXXXX 250 - 300 : [ 2116 0.03 0.11 ] |XXXXXXX 300 - 350 : [ 2209 0.03 0.13 ] |XXXXXXX 350 - 400 : [ 2459 0.03 0.16 ] |XXXXXXXX 400 - 450 : [ 2834 0.03 0.20 ] |XXXXXXXXXX 450 - 500 : [ 3233 0.04 0.24 ] |XXXXXXXXXXXX 500 - 550 : [ 4077 0.05 0.28 ] |XXXXXXXXXXXXXXXX 550 - 600 : [ 5449 0.07 0.35 ] |XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 7548 0.09 0.44 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 10080 0.12 0.56 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 12698 0.15 0.72 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 13506 0.16 0.88 ] |XXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 8050 0.10 0.98 ] |XXXXX 850 - 900 : [ 1709 0.02 1.00 ] | 900 - 950 : [ 59 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZF Command: /usr/xpg4/bin/grep AHZF 3634482_fasta.screen.screen.ids > reads.trim15.AHZF.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZF.rl 2 50 #Found 36793 total values totalling 25280775.0000. <687.108281 +/- 161.646511> #Range: [ 22 - 937 ] #Most likely bin: [ 750 - 800 ] 8926 counts #Median bin: [ 700 - 750 ] 6297 counts | 0 - 50 : [ 35 0.00 0.00 ] |X 50 - 100 : [ 140 0.00 0.00 ] |X 100 - 150 : [ 275 0.01 0.01 ] |XX 150 - 200 : [ 364 0.01 0.02 ] |XX 200 - 250 : [ 440 0.01 0.03 ] |XX 250 - 300 : [ 491 0.01 0.05 ] |XX 300 - 350 : [ 551 0.01 0.06 ] |XXX 350 - 400 : [ 653 0.02 0.08 ] |XXX 400 - 450 : [ 766 0.02 0.10 ] |XXXX 450 - 500 : [ 862 0.02 0.12 ] |XXXXX 500 - 550 : [ 1089 0.03 0.15 ] |XXXXXXX 550 - 600 : [ 1557 0.04 0.20 ] |XXXXXXXXXXX 600 - 650 : [ 2449 0.07 0.26 ] |XXXXXXXXXXXXXXXXXX 650 - 700 : [ 3906 0.11 0.37 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 6297 0.17 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 8926 0.24 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 6391 0.17 0.96 ] |XXXXXXX 850 - 900 : [ 1542 0.04 1.00 ] | 900 - 950 : [ 59 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZG Command: /usr/xpg4/bin/grep AHZG 3634482_fasta.screen.screen.ids > reads.trim15.AHZG.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZG.rl 2 50 #Found 40150 total values totalling 21984321.0000. <547.554695 +/- 202.230148> #Range: [ 22 - 896 ] #Most likely bin: [ 700 - 750 ] 5382 counts #Median bin: [ 600 - 650 ] 4542 counts |XX 0 - 50 : [ 206 0.01 0.01 ] |XXXXXXX 50 - 100 : [ 990 0.02 0.03 ] |XXXXXXXXX 100 - 150 : [ 1209 0.03 0.06 ] |XXXXXXXXX 150 - 200 : [ 1164 0.03 0.09 ] |XXXXXXXXX 200 - 250 : [ 1269 0.03 0.12 ] |XXXXXXXXXX 250 - 300 : [ 1341 0.03 0.15 ] |XXXXXXXXXXX 300 - 350 : [ 1443 0.04 0.19 ] |XXXXXXXXXXXX 350 - 400 : [ 1656 0.04 0.23 ] |XXXXXXXXXXXXXX 400 - 450 : [ 1901 0.05 0.28 ] |XXXXXXXXXXXXXXXX 450 - 500 : [ 2172 0.05 0.33 ] |XXXXXXXXXXXXXXXXXXXX 500 - 550 : [ 2724 0.07 0.40 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 550 - 600 : [ 3501 0.09 0.49 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 4542 0.11 0.60 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 5378 0.13 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 5382 0.13 0.87 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 3753 0.09 0.96 ] |XXXXXXXXXX 800 - 850 : [ 1373 0.03 1.00 ] |X 850 - 900 : [ 146 0.00 1.00 ] JAZZ trim 15 readlength histogram for AHZH Command: /usr/xpg4/bin/grep AHZH 3634482_fasta.screen.screen.ids > reads.trim15.AHZH.rl Command: /home/copeland/scripts/histogram2.pl reads.trim15.AHZH.rl 2 50 #Found 5692 total values totalling 3327040.0000. <584.511595 +/- 201.663100> #Range: [ 29 - 879 ] #Most likely bin: [ 700 - 750 ] 1019 counts #Median bin: [ 650 - 700 ] 796 counts |X 0 - 50 : [ 21 0.00 0.00 ] |XXXXX 50 - 100 : [ 123 0.02 0.03 ] |XXXXX 100 - 150 : [ 126 0.02 0.05 ] |XXXXX 150 - 200 : [ 116 0.02 0.07 ] |XXXXX 200 - 250 : [ 130 0.02 0.09 ] |XXXXXXXXXXX 250 - 300 : [ 284 0.05 0.14 ] |XXXXXXXX 300 - 350 : [ 215 0.04 0.18 ] |XXXXXX 350 - 400 : [ 150 0.03 0.20 ] |XXXXXXX 400 - 450 : [ 167 0.03 0.23 ] |XXXXXXXX 450 - 500 : [ 199 0.03 0.27 ] |XXXXXXXXXX 500 - 550 : [ 264 0.05 0.32 ] |XXXXXXXXXXXXXXX 550 - 600 : [ 391 0.07 0.38 ] |XXXXXXXXXXXXXXXXXXXXXX 600 - 650 : [ 557 0.10 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 650 - 700 : [ 796 0.14 0.62 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1019 0.18 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 827 0.15 0.95 ] |XXXXXXXXXXX 800 - 850 : [ 286 0.05 1.00 ] |X 850 - 900 : [ 21 0.00 1.00 ] JAZZ trim 15 readlength histogram for APZI JAZZ trim 15 readlength histogram for APZK ################################################################### GC content histogram Command: /bin/nawk '{print $5+$6}' GC.3634482_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005 ------------------------------------------------------------------- # GC.3634482_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005 #Found 82351 total values totalling 57142.3309. <0.693888 +/- 0.042728> #Range: [ 0 - 0.9286 ] #Most likely bin: [ 0.7 - 0.705 ] 4383 counts #Median bin: [ 0.695 - 0.7 ] 4283 counts | 0 - 0.005 : [ 1 0.00 0.00 ] #... | 0.185 - 0.19 : [ 1 0.00 0.00 ] #... | 0.3 - 0.305 : [ 3 0.00 0.00 ] #... | 0.325 - 0.33 : [ 1 0.00 0.00 ] | 0.33 - 0.335 : [ 1 0.00 0.00 ] #... | 0.35 - 0.355 : [ 1 0.00 0.00 ] #... | 0.37 - 0.375 : [ 2 0.00 0.00 ] #... | 0.39 - 0.395 : [ 3 0.00 0.00 ] | 0.395 - 0.4 : [ 2 0.00 0.00 ] | 0.4 - 0.405 : [ 1 0.00 0.00 ] | 0.405 - 0.41 : [ 4 0.00 0.00 ] | 0.41 - 0.415 : [ 1 0.00 0.00 ] #... | 0.42 - 0.425 : [ 4 0.00 0.00 ] | 0.425 - 0.43 : [ 5 0.00 0.00 ] | 0.43 - 0.435 : [ 7 0.00 0.00 ] #... | 0.44 - 0.445 : [ 9 0.00 0.00 ] | 0.445 - 0.45 : [ 1 0.00 0.00 ] | 0.45 - 0.455 : [ 1 0.00 0.00 ] | 0.455 - 0.46 : [ 2 0.00 0.00 ] | 0.46 - 0.465 : [ 7 0.00 0.00 ] | 0.465 - 0.47 : [ 5 0.00 0.00 ] | 0.47 - 0.475 : [ 3 0.00 0.00 ] | 0.475 - 0.48 : [ 6 0.00 0.00 ] | 0.48 - 0.485 : [ 13 0.00 0.00 ] | 0.485 - 0.49 : [ 7 0.00 0.00 ] | 0.49 - 0.495 : [ 3 0.00 0.00 ] | 0.495 - 0.5 : [ 3 0.00 0.00 ] | 0.5 - 0.505 : [ 18 0.00 0.00 ] | 0.505 - 0.51 : [ 12 0.00 0.00 ] | 0.51 - 0.515 : [ 21 0.00 0.00 ] | 0.515 - 0.52 : [ 16 0.00 0.00 ] | 0.52 - 0.525 : [ 26 0.00 0.00 ] | 0.525 - 0.53 : [ 17 0.00 0.00 ] | 0.53 - 0.535 : [ 32 0.00 0.00 ] | 0.535 - 0.54 : [ 44 0.00 0.00 ] | 0.54 - 0.545 : [ 40 0.00 0.00 ] |X 0.545 - 0.55 : [ 59 0.00 0.00 ] |X 0.55 - 0.555 : [ 73 0.00 0.01 ] |X 0.555 - 0.56 : [ 80 0.00 0.01 ] |X 0.56 - 0.565 : [ 120 0.00 0.01 ] |X 0.565 - 0.57 : [ 129 0.00 0.01 ] |X 0.57 - 0.575 : [ 145 0.00 0.01 ] |XX 0.575 - 0.58 : [ 204 0.00 0.01 ] |XX 0.58 - 0.585 : [ 203 0.00 0.02 ] |XX 0.585 - 0.59 : [ 231 0.00 0.02 ] |XX 0.59 - 0.595 : [ 268 0.00 0.02 ] |XX 0.595 - 0.6 : [ 253 0.00 0.03 ] |XXX 0.6 - 0.605 : [ 356 0.00 0.03 ] |XXX 0.605 - 0.61 : [ 368 0.00 0.03 ] |XXXX 0.61 - 0.615 : [ 468 0.01 0.04 ] |XXXXX 0.615 - 0.62 : [ 586 0.01 0.05 ] |XXXXXX 0.62 - 0.625 : [ 649 0.01 0.05 ] |XXXXXXXX 0.625 - 0.63 : [ 903 0.01 0.07 ] |XXXXXXXXX 0.63 - 0.635 : [ 993 0.01 0.08 ] |XXXXXXXXXXX 0.635 - 0.64 : [ 1165 0.01 0.09 ] |XXXXXXXXXXXXX 0.64 - 0.645 : [ 1387 0.02 0.11 ] |XXXXXXXXXXXXXXX 0.645 - 0.65 : [ 1680 0.02 0.13 ] |XXXXXXXXXXXXXXXXXX 0.65 - 0.655 : [ 1929 0.02 0.15 ] |XXXXXXXXXXXXXXXXXXXXX 0.655 - 0.66 : [ 2297 0.03 0.18 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 0.66 - 0.665 : [ 2698 0.03 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.665 - 0.67 : [ 3031 0.04 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.67 - 0.675 : [ 3343 0.04 0.29 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.675 - 0.68 : [ 3563 0.04 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.68 - 0.685 : [ 3886 0.05 0.38 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.685 - 0.69 : [ 4171 0.05 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.69 - 0.695 : [ 4245 0.05 0.48 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.695 - 0.7 : [ 4283 0.05 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.7 - 0.705 : [ 4383 0.05 0.59 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.705 - 0.71 : [ 4220 0.05 0.64 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.71 - 0.715 : [ 4088 0.05 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.715 - 0.72 : [ 3752 0.05 0.74 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.72 - 0.725 : [ 3798 0.05 0.78 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.725 - 0.73 : [ 3235 0.04 0.82 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.73 - 0.735 : [ 2928 0.04 0.86 ] |XXXXXXXXXXXXXXXXXXXXXX 0.735 - 0.74 : [ 2443 0.03 0.89 ] |XXXXXXXXXXXXXXXXXXX 0.74 - 0.745 : [ 2030 0.02 0.91 ] |XXXXXXXXXXXXXX 0.745 - 0.75 : [ 1515 0.02 0.93 ] |XXXXXXXXXXXXX 0.75 - 0.755 : [ 1421 0.02 0.95 ] |XXXXXXXXX 0.755 - 0.76 : [ 1012 0.01 0.96 ] |XXXXXXX 0.76 - 0.765 : [ 810 0.01 0.97 ] |XXXXXX 0.765 - 0.77 : [ 618 0.01 0.98 ] |XXXX 0.77 - 0.775 : [ 492 0.01 0.98 ] |XXX 0.775 - 0.78 : [ 354 0.00 0.99 ] |XX 0.78 - 0.785 : [ 267 0.00 0.99 ] |XX 0.785 - 0.79 : [ 202 0.00 0.99 ] |XX 0.79 - 0.795 : [ 170 0.00 0.99 ] |X 0.795 - 0.8 : [ 89 0.00 0.99 ] |X 0.8 - 0.805 : [ 106 0.00 1.00 ] |X 0.805 - 0.81 : [ 64 0.00 1.00 ] | 0.81 - 0.815 : [ 50 0.00 1.00 ] | 0.815 - 0.82 : [ 40 0.00 1.00 ] | 0.82 - 0.825 : [ 29 0.00 1.00 ] | 0.825 - 0.83 : [ 26 0.00 1.00 ] | 0.83 - 0.835 : [ 19 0.00 1.00 ] | 0.835 - 0.84 : [ 16 0.00 1.00 ] | 0.84 - 0.845 : [ 16 0.00 1.00 ] | 0.845 - 0.85 : [ 3 0.00 1.00 ] | 0.85 - 0.855 : [ 11 0.00 1.00 ] | 0.855 - 0.86 : [ 6 0.00 1.00 ] | 0.86 - 0.865 : [ 15 0.00 1.00 ] | 0.865 - 0.87 : [ 4 0.00 1.00 ] | 0.87 - 0.875 : [ 1 0.00 1.00 ] | 0.875 - 0.88 : [ 4 0.00 1.00 ] | 0.88 - 0.885 : [ 7 0.00 1.00 ] | 0.885 - 0.89 : [ 3 0.00 1.00 ] | 0.89 - 0.895 : [ 3 0.00 1.00 ] | 0.895 - 0.9 : [ 1 0.00 1.00 ] | 0.9 - 0.905 : [ 1 0.00 1.00 ] | 0.905 - 0.91 : [ 5 0.00 1.00 ] | 0.91 - 0.915 : [ 2 0.00 1.00 ] | 0.915 - 0.92 : [ 1 0.00 1.00 ] | 0.92 - 0.925 : [ 1 0.00 1.00 ] | 0.925 - 0.93 : [ 1 0.00 1.00 ] ################################################################### reads2plates summary plate(s) reads clones N/plate avg% LIBRARY @ 256 40151 21881 85.47 89.03 AHZG @ 36 5692 3119 86.64 90.25 AHZH @ 200 36793 18756 93.78 97.69 AHZF @ ] 82636 43756 88.93 cumulative total@@ LIBRARY PLATE ID COUNT [ AHZG 256 AHZH 36 AHZF 200 ] for 492 total 96 well plate ids. 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 = 1548 HQ Discrepant reads = 127 Chimeric reads = 435 Suspect alignments = 5967 ################################################################### C O N T I G I N F O R M A T I O N Mon Sep 6 05:41:38 2004 File: /psf/project/genome3/3634482/edit_dir.06Jul04.QD/phrap.out Contig 163. 922 reads; 50687 bp (untrimmed), 50504 (trimmed). Contig 164. 944 reads; 67709 bp (untrimmed), 67312 (trimmed). Contig 165. 962 reads; 64602 bp (untrimmed), 64139 (trimmed). Contig 166. 982 reads; 66309 bp (untrimmed), 65981 (trimmed). Contig 167. 999 reads; 67262 bp (untrimmed), 66929 (trimmed). Contig 168. 1026 reads; 71556 bp (untrimmed), 70729 (trimmed). Contig 169. 1100 reads; 69270 bp (untrimmed), 69229 (trimmed). Contig 170. 1110 reads; 66398 bp (untrimmed), 66237 (trimmed). Contig 171. 1117 reads; 72132 bp (untrimmed), 71633 (trimmed). Contig 172. 1266 reads; 91433 bp (untrimmed), 90676 (trimmed). Contig 173. 1303 reads; 77363 bp (untrimmed), 76728 (trimmed). Contig 174. 1338 reads; 88831 bp (untrimmed), 88004 (trimmed). Contig 175. 1443 reads; 96672 bp (untrimmed), 96583 (trimmed). Contig 176. 1447 reads; 104633 bp (untrimmed), 103210 (trimmed). Contig 177. 1471 reads; 92186 bp (untrimmed), 92029 (trimmed). Contig 178. 1744 reads; 109406 bp (untrimmed), 109034 (trimmed). Contig 179. 1767 reads; 110659 bp (untrimmed), 110532 (trimmed). Contig 180. 1799 reads; 102730 bp (untrimmed), 101864 (trimmed). Contig 181. 2134 reads; 125808 bp (untrimmed), 124729 (trimmed). Contig 182. 2138 reads; 125683 bp (untrimmed), 125657 (trimmed). Contig 183. 2450 reads; 190489 bp (untrimmed), 189982 (trimmed). Contig 184. 2597 reads; 161260 bp (untrimmed), 160544 (trimmed). Contig 185. 3031 reads; 183375 bp (untrimmed), 182913 (trimmed). Contig 186. 3494 reads; 207246 bp (untrimmed), 207232 (trimmed). Contig 187. 3896 reads; 238722 bp (untrimmed), 238166 (trimmed). Contig 188. 4186 reads; 290500 bp (untrimmed), 289449 (trimmed). Contig 189. 9034 reads; 539509 bp (untrimmed), 538962 (trimmed). -------------------------------------------------------------- Totals 82561 reads; 5508577 bp (untrimmed), 5431277 (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 123 total values totalling 5379665.0000. <43737.113821 +/- 66660.719175> #Range: [ 2247 - 538962 ] #Most likely bin: [ 2000 - 4000 ] 16 counts #Median bin: [ 24000 - 26000 ] 5 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2000 - 4000 : [ 16 0.13 0.13 ] |XXXXXXXXXXXXXXXXXXXXXX 4000 - 6000 : [ 9 0.07 0.20 ] |XXXXXXXXXXXXXXX 6000 - 8000 : [ 6 0.05 0.25 ] |XXXXX 8000 - 10000 : [ 2 0.02 0.27 ] |XXXXXXXXXXXXXXXXXXXXXX 10000 - 12000 : [ 9 0.07 0.34 ] |XXXXXXXXXX 12000 - 14000 : [ 4 0.03 0.37 ] |XXXXXXXXXXXX 14000 - 16000 : [ 5 0.04 0.41 ] |XXXXX 16000 - 18000 : [ 2 0.02 0.43 ] #... |XXXXXXXX 20000 - 22000 : [ 3 0.02 0.46 ] |XXXXXXXXXX 22000 - 24000 : [ 4 0.03 0.49 ] |XXXXXXXXXXXX 24000 - 26000 : [ 5 0.04 0.53 ] |XXXXXXXXXX 26000 - 28000 : [ 4 0.03 0.56 ] |XXXXXXXXXXXX 28000 - 30000 : [ 5 0.04 0.60 ] |XXXXX 30000 - 32000 : [ 2 0.02 0.62 ] |XX 32000 - 34000 : [ 1 0.01 0.63 ] |XXXXXXXX 34000 - 36000 : [ 3 0.02 0.65 ] |XXXXX 36000 - 38000 : [ 2 0.02 0.67 ] |XXXXX 38000 - 40000 : [ 2 0.02 0.68 ] |XXXXXXXXXXXX 40000 - 42000 : [ 5 0.04 0.72 ] |XX 42000 - 44000 : [ 1 0.01 0.73 ] #... |XX 46000 - 48000 : [ 1 0.01 0.74 ] #... |XXXXXXXX 50000 - 52000 : [ 3 0.02 0.76 ] |XX 52000 - 54000 : [ 1 0.01 0.77 ] |XX 54000 - 56000 : [ 1 0.01 0.78 ] |XX 56000 - 58000 : [ 1 0.01 0.79 ] #... |XXXXX 64000 - 66000 : [ 2 0.02 0.80 ] |XXXXXXXX 66000 - 68000 : [ 3 0.02 0.83 ] |XX 68000 - 70000 : [ 1 0.01 0.84 ] |XXXXX 70000 - 72000 : [ 2 0.02 0.85 ] #... |XX 76000 - 78000 : [ 1 0.01 0.86 ] #... |XX 88000 - 90000 : [ 1 0.01 0.87 ] |XX 90000 - 92000 : [ 1 0.01 0.88 ] |XX 92000 - 94000 : [ 1 0.01 0.89 ] #... |XX 96000 - 98000 : [ 1 0.01 0.89 ] #... |XX 100000 - 102000 : [ 1 0.01 0.90 ] |XX 102000 - 104000 : [ 1 0.01 0.91 ] #... |XX 108000 - 110000 : [ 1 0.01 0.92 ] |XX 110000 - 112000 : [ 1 0.01 0.93 ] #... |XXXXX 124000 - 126000 : [ 2 0.02 0.94 ] #... |XX 160000 - 162000 : [ 1 0.01 0.95 ] #... |XX 182000 - 184000 : [ 1 0.01 0.96 ] #... |XX 188000 - 190000 : [ 1 0.01 0.97 ] #... |XX 206000 - 208000 : [ 1 0.01 0.98 ] #... |XX 238000 - 240000 : [ 1 0.01 0.98 ] #... |XX 288000 - 290000 : [ 1 0.01 0.99 ] #... |XX 538000 - 540000 : [ 1 0.01 1.00 ] ################################################################### Base Count for Project: ------------------------------------------------------------------- A = 12356098 C = 26813841 G = 26209050 T = 13102332 N = 440588 X = 1369137 GC fraction = 0.66 Total = 80291046 ################################################################### Base Count for contigs: ------------------------------------------------------------------- 3634482_fasta.screen.contigs A 843407 C 1950823 G 1897472 N 223 T 816112 X 540 fraction GC = 0.70 total bases = 5508577 ################################################################### Depth Summary: ------------------------------------------------------------------- depth.out contains 5488650 bases = 12.70 +- 5.30 = 0.32 +- 3.94 m1 = 2.21 m2 = 3.13 ################################################################### Histogram of All Contig Depth Values: Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 ------------------------------------------------------------------- #Found 165 total values totalling 1520.6400. <9.216000 +/- 4.446577> #Range: [ 1.08 - 15.98 ] #Most likely bin: [ 12 - 12.5 ] 15 counts #Median bin: [ 10.5 - 11 ] 3 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 11 0.07 0.07 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 10 0.06 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 9 0.05 0.18 ] |XXXXXXXXXXX 2.5 - 3 : [ 4 0.02 0.21 ] |XXX 3 - 3.5 : [ 1 0.01 0.21 ] |XXX 3.5 - 4 : [ 1 0.01 0.22 ] #... |XXX 4.5 - 5 : [ 1 0.01 0.22 ] |XXXXX 5 - 5.5 : [ 2 0.01 0.24 ] |XXXXX 5.5 - 6 : [ 2 0.01 0.25 ] |XXXXXXXX 6 - 6.5 : [ 3 0.02 0.27 ] |XXXXX 6.5 - 7 : [ 2 0.01 0.28 ] |XXXXXXXX 7 - 7.5 : [ 3 0.02 0.30 ] |XXXXX 7.5 - 8 : [ 2 0.01 0.31 ] |XXXXXXXXXXXXX 8 - 8.5 : [ 5 0.03 0.34 ] |XXXXXXXXXXX 8.5 - 9 : [ 4 0.02 0.36 ] |XXXXXXXXXXXXX 9 - 9.5 : [ 5 0.03 0.39 ] |XXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.04 0.43 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 11 0.07 0.50 ] |XXXXXXXX 10.5 - 11 : [ 3 0.02 0.52 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.07 0.59 ] |XXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.04 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 15 0.09 0.72 ] |XXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 8 0.05 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 13 0.08 0.85 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.06 0.91 ] |XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 9 0.05 0.96 ] |XXXXXXXX 14.5 - 15 : [ 3 0.02 0.98 ] |XXXXX 15 - 15.5 : [ 2 0.01 0.99 ] |XXX 15.5 - 16 : [ 1 0.01 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 124 total values totalling 1397.2400. <11.268065 +/- 2.664983> #Range: [ 2.09 - 15.98 ] #Most likely bin: [ 12 - 12.5 ] 15 counts #Median bin: [ 11.5 - 12 ] 7 counts |XXX 2 - 2.5 : [ 1 0.01 0.01 ] #... |XXX 3.5 - 4 : [ 1 0.01 0.02 ] #... |XXX 4.5 - 5 : [ 1 0.01 0.02 ] |XXXXX 5 - 5.5 : [ 2 0.02 0.04 ] |XXXXX 5.5 - 6 : [ 2 0.02 0.06 ] |XXXXXXXX 6 - 6.5 : [ 3 0.02 0.08 ] |XXXXX 6.5 - 7 : [ 2 0.02 0.10 ] |XXXXX 7 - 7.5 : [ 2 0.02 0.11 ] |XXX 7.5 - 8 : [ 1 0.01 0.12 ] |XXXXXXXXXXX 8 - 8.5 : [ 4 0.03 0.15 ] |XXXXX 8.5 - 9 : [ 2 0.02 0.17 ] |XXXXXXXXXXX 9 - 9.5 : [ 4 0.03 0.20 ] |XXXXXXXXXXXXXXXX 9.5 - 10 : [ 6 0.05 0.25 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 10 - 10.5 : [ 10 0.08 0.33 ] |XXXXXXXX 10.5 - 11 : [ 3 0.02 0.35 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 11 - 11.5 : [ 12 0.10 0.45 ] |XXXXXXXXXXXXXXXXXXX 11.5 - 12 : [ 7 0.06 0.51 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 12 - 12.5 : [ 15 0.12 0.63 ] |XXXXXXXXXXXXXXXXXXXXX 12.5 - 13 : [ 8 0.06 0.69 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 13 - 13.5 : [ 13 0.10 0.80 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 13.5 - 14 : [ 10 0.08 0.88 ] |XXXXXXXXXXXXXXXXXXXXXXXX 14 - 14.5 : [ 9 0.07 0.95 ] |XXXXXXXX 14.5 - 15 : [ 3 0.02 0.98 ] |XXXXX 15 - 15.5 : [ 2 0.02 0.99 ] |XXX 15.5 - 16 : [ 1 0.01 1.00 ] ################################################################### Sorted Depth Values: ------------------------------------------------------------------- Contig 22 2 reads 2059 bases = 1.08 +- 0.27 = 0.02 +- 0.96 m1 = 0.07 m2 = -0.21 Contig 37 2 reads 1690 bases = 1.10 +- 0.30 = -0.00 +- 0.95 m1 = 0.08 m2 = -0.20 Contig 28 2 reads 1101 bases = 1.15 +- 0.36 = -0.25 +- 0.89 m1 = 0.11 m2 = -0.16 Contig 33 2 reads 1108 bases = 1.18 +- 0.39 = 1.18 +- 0.39 m1 = 0.13 m2 = 0.00 Contig 24 2 reads 1654 bases = 1.20 +- 0.40 = -0.02 +- 0.89 m1 = 0.13 m2 = -0.16 Contig 25 2 reads 1722 bases = 1.21 +- 0.40 = -0.02 +- 0.89 m1 = 0.14 m2 = -0.16 Contig 32 2 reads 1086 bases = 1.22 +- 0.42 = 1.22 +- 0.42 m1 = 0.14 m2 = 0.00 Contig 31 2 reads 981 bases = 1.31 +- 0.46 = 0.69 +- 0.46 m1 = 0.16 m2 = -0.00 Contig 38 2 reads 769 bases = 1.31 +- 0.46 = 1.31 +- 0.46 m1 = 0.16 m2 = 0.00 Contig 36 2 reads 1141 bases = 1.32 +- 0.47 = 1.32 +- 0.47 m1 = 0.16 m2 = 0.00 Contig 21 2 reads 1220 bases = 1.49 +- 0.50 = 1.49 +- 0.50 m1 = 0.17 m2 = 0.00 Contig 35 2 reads 878 bases = 1.57 +- 0.49 = 1.57 +- 0.49 m1 = 0.16 m2 = 0.00 Contig 58 12 reads 1031 bases = 1.63 +- 2.51 = 1.63 +- 2.51 m1 = 3.85 m2 = 0.00 Contig 23 2 reads 1015 bases = 1.67 +- 0.47 = 1.67 +- 0.47 m1 = 0.13 m2 = 0.00 Contig 40 2 reads 1185 bases = 1.69 +- 0.46 = -0.04 +- 0.55 m1 = 0.13 m2 = -0.02 Contig 43 3 reads 986 bases = 1.73 +- 0.85 = 1.73 +- 0.85 m1 = 0.42 m2 = 0.00 Contig 47 4 reads 1482 bases = 1.90 +- 1.11 = 1.90 +- 1.11 m1 = 0.65 m2 = 0.00 Contig 27 2 reads 757 bases = 1.93 +- 0.26 = 0.01 +- 0.27 m1 = 0.03 m2 = -0.00 Contig 26 2 reads 584 bases = 1.95 +- 0.22 = -0.02 +- 0.22 m1 = 0.02 m2 = -0.00 Contig 20 2 reads 798 bases = 1.96 +- 0.20 = -0.02 +- 0.20 m1 = 0.02 m2 = -0.00 Contig 155 613 reads 38699 bases = 13.67 +- 4.74 = 0.25 +- 3.99 m1 = 1.64 m2 = 1.63 Contig 187 3896 reads 238722 bases = 13.70 +- 4.89 = 0.37 +- 4.34 m1 = 1.74 m2 = 1.28 Contig 90 79 reads 4704 bases = 13.77 +- 5.84 = 0.89 +- 3.62 m1 = 2.48 m2 = 5.26 Contig 185 3031 reads 183375 bases = 13.84 +- 4.62 = 0.29 +- 3.93 m1 = 1.54 m2 = 1.47 Contig 96 91 reads 5882 bases = 13.92 +- 7.56 = 2.49 +- 3.19 m1 = 4.11 m2 = 11.75 Contig 115 216 reads 13655 bases = 14.03 +- 5.38 = 0.58 +- 4.71 m1 = 2.06 m2 = 1.67 Contig 181 2134 reads 125808 bases = 14.17 +- 5.53 = 0.45 +- 4.12 m1 = 2.16 m2 = 3.42 Contig 110 178 reads 10866 bases = 14.27 +- 4.06 = 0.80 +- 3.84 m1 = 1.15 m2 = 0.43 Contig 135 398 reads 23931 bases = 14.29 +- 5.14 = 0.22 +- 3.82 m1 = 1.85 m2 = 2.95 Contig 173 1303 reads 77363 bases = 14.31 +- 5.20 = 0.37 +- 4.30 m1 = 1.89 m2 = 2.14 Contig 189 9034 reads 539509 bases = 14.31 +- 6.84 = 0.22 +- 4.36 m1 = 3.27 m2 = 6.94 Contig 186 3494 reads 207246 bases = 14.32 +- 5.01 = 0.18 +- 4.17 m1 = 1.75 m2 = 1.94 Contig 182 2138 reads 125683 bases = 14.38 +- 4.56 = 0.06 +- 3.83 m1 = 1.45 m2 = 1.53 Contig 170 1110 reads 66398 bases = 14.44 +- 4.57 = 0.55 +- 3.99 m1 = 1.44 m2 = 1.22 Contig 94 83 reads 4906 bases = 14.50 +- 5.03 = 0.49 +- 3.47 m1 = 1.74 m2 = 3.31 Contig 132 391 reads 22910 bases = 14.67 +- 5.26 = 0.98 +- 4.26 m1 = 1.89 m2 = 2.38 Contig 180 1799 reads 102730 bases = 14.74 +- 5.04 = 0.20 +- 4.13 m1 = 1.72 m2 = 2.09 Contig 144 490 reads 27352 bases = 15.16 +- 8.63 = 0.23 +- 4.73 m1 = 4.91 m2 = 13.03 Contig 150 541 reads 30873 bases = 15.31 +- 4.71 = 0.32 +- 4.26 m1 = 1.45 m2 = 1.01 Contig 163 922 reads 50687 bases = 15.98 +- 5.46 = 0.43 +- 4.74 m1 = 1.86 m2 = 1.84 ################################################################### Histogram of Number of Reads per Contig: Command: hist contig.grep 3 1 ------------------------------------------------------------------- #Found 189 total values totalling 82561.0000. <436.830688 +/- 931.167011> #Range: [ 1 - 9034 ] #Most likely bin: [ 2 - 3 ] 23 counts #Median bin: [ 84 - 85 ] 1 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1 - 2 : [ 18 0.10 0.10 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 3 : [ 23 0.12 0.22 ] |XXXXX 3 - 4 : [ 3 0.02 0.23 ] |XXXXXXXXXX 4 - 5 : [ 6 0.03 0.26 ] |XX 5 - 6 : [ 1 0.01 0.27 ] |XXX 6 - 7 : [ 2 0.01 0.28 ] |XX 7 - 8 : [ 1 0.01 0.29 ] |XX 8 - 9 : [ 1 0.01 0.29 ] |XX 9 - 10 : [ 1 0.01 0.30 ] |XX 10 - 11 : [ 1 0.01 0.30 ] #... |XX 12 - 13 : [ 1 0.01 0.31 ] #... |XXX 15 - 16 : [ 2 0.01 0.32 ] #... |XX 17 - 18 : [ 1 0.01 0.32 ] |XXXXX 18 - 19 : [ 3 0.02 0.34 ] |XXX 19 - 20 : [ 2 0.01 0.35 ] |XX 20 - 21 : [ 1 0.01 0.35 ] |XXXXX 21 - 22 : [ 3 0.02 0.37 ] |XX 22 - 23 : [ 1 0.01 0.38 ] #... |XX 24 - 25 : [ 1 0.01 0.38 ] #... |XXX 28 - 29 : [ 2 0.01 0.39 ] #... |XXX 34 - 35 : [ 2 0.01 0.40 ] #... |XX 37 - 38 : [ 1 0.01 0.41 ] #... |XX 40 - 41 : [ 1 0.01 0.41 ] |XXX 41 - 42 : [ 2 0.01 0.42 ] |XX 42 - 43 : [ 1 0.01 0.43 ] #... |XX 44 - 45 : [ 1 0.01 0.43 ] |XX 45 - 46 : [ 1 0.01 0.44 ] #... |XXX 47 - 48 : [ 2 0.01 0.45 ] #... |XX 51 - 52 : [ 1 0.01 0.46 ] #... |XX 71 - 72 : [ 1 0.01 0.46 ] #... |XX 73 - 74 : [ 1 0.01 0.47 ] |XX 74 - 75 : [ 1 0.01 0.47 ] #... |XX 79 - 80 : [ 1 0.01 0.48 ] #... |XX 81 - 82 : [ 1 0.01 0.48 ] |XXX 82 - 83 : [ 2 0.01 0.49 ] |XX 83 - 84 : [ 1 0.01 0.50 ] |XX 84 - 85 : [ 1 0.01 0.50 ] #... |XX 91 - 92 : [ 1 0.01 0.51 ] #... |XX 110 - 111 : [ 1 0.01 0.51 ] |XX 111 - 112 : [ 1 0.01 0.52 ] #... |XX 113 - 114 : [ 1 0.01 0.52 ] |XX 114 - 115 : [ 1 0.01 0.53 ] #... |XX 126 - 127 : [ 1 0.01 0.53 ] #... |XX 130 - 131 : [ 1 0.01 0.54 ] #... |XX 138 - 139 : [ 1 0.01 0.54 ] #... |XX 143 - 144 : [ 1 0.01 0.55 ] #... |XX 147 - 148 : [ 1 0.01 0.56 ] #... |XXX 156 - 157 : [ 2 0.01 0.57 ] #... |XX 165 - 166 : [ 1 0.01 0.57 ] #... |XX 176 - 177 : [ 1 0.01 0.58 ] #... |XX 178 - 179 : [ 1 0.01 0.58 ] #... |XX 184 - 185 : [ 1 0.01 0.59 ] #... |XX 187 - 188 : [ 1 0.01 0.59 ] #... |XX 201 - 202 : [ 1 0.01 0.60 ] #... |XX 212 - 213 : [ 1 0.01 0.60 ] #... |XX 216 - 217 : [ 1 0.01 0.61 ] #... |XX 218 - 219 : [ 1 0.01 0.61 ] #... |XX 230 - 231 : [ 1 0.01 0.62 ] #... |XX 242 - 243 : [ 1 0.01 0.62 ] #... |XX 260 - 261 : [ 1 0.01 0.63 ] #... |XX 268 - 269 : [ 1 0.01 0.63 ] #... |XX 271 - 272 : [ 1 0.01 0.64 ] #... |XX 336 - 337 : [ 1 0.01 0.65 ] #... |XX 345 - 346 : [ 1 0.01 0.65 ] #... |XX 348 - 349 : [ 1 0.01 0.66 ] #... |XX 355 - 356 : [ 1 0.01 0.66 ] #... |XX 359 - 360 : [ 1 0.01 0.67 ] |XX 360 - 361 : [ 1 0.01 0.67 ] #... |XX 370 - 371 : [ 1 0.01 0.68 ] #... |XX 376 - 377 : [ 1 0.01 0.68 ] #... |XX 390 - 391 : [ 1 0.01 0.69 ] |XXX 391 - 392 : [ 2 0.01 0.70 ] #... |XXX 396 - 397 : [ 2 0.01 0.71 ] #... |XX 398 - 399 : [ 1 0.01 0.71 ] #... |XX 418 - 419 : [ 1 0.01 0.72 ] |XX 419 - 420 : [ 1 0.01 0.72 ] #... |XXX 424 - 425 : [ 2 0.01 0.74 ] #... |XX 428 - 429 : [ 1 0.01 0.74 ] #... |XX 444 - 445 : [ 1 0.01 0.75 ] #... |XX 450 - 451 : [ 1 0.01 0.75 ] #... |XX 464 - 465 : [ 1 0.01 0.76 ] #... |XX 490 - 491 : [ 1 0.01 0.76 ] #... |XXX 524 - 525 : [ 2 0.01 0.77 ] #... |XX 527 - 528 : [ 1 0.01 0.78 ] #... |XX 539 - 540 : [ 1 0.01 0.78 ] |XX 540 - 541 : [ 1 0.01 0.79 ] |XX 541 - 542 : [ 1 0.01 0.79 ] #... |XX 559 - 560 : [ 1 0.01 0.80 ] #... |XX 588 - 589 : [ 1 0.01 0.80 ] #... |XX 600 - 601 : [ 1 0.01 0.81 ] #... |XX 605 - 606 : [ 1 0.01 0.81 ] #... |XX 613 - 614 : [ 1 0.01 0.82 ] #... |XX 621 - 622 : [ 1 0.01 0.83 ] #... |XX 666 - 667 : [ 1 0.01 0.83 ] #... |XX 733 - 734 : [ 1 0.01 0.84 ] #... |XX 747 - 748 : [ 1 0.01 0.84 ] #... |XX 780 - 781 : [ 1 0.01 0.85 ] #... |XX 840 - 841 : [ 1 0.01 0.85 ] #... |XX 903 - 904 : [ 1 0.01 0.86 ] #... |XX 922 - 923 : [ 1 0.01 0.86 ] #... |XX 944 - 945 : [ 1 0.01 0.87 ] #... |XX 962 - 963 : [ 1 0.01 0.87 ] #... |XX 982 - 983 : [ 1 0.01 0.88 ] #... |XX 999 - 1000 : [ 1 0.01 0.88 ] #... |XX 1026 - 1027 : [ 1 0.01 0.89 ] #... |XX 1100 - 1101 : [ 1 0.01 0.89 ] #... |XX 1110 - 1111 : [ 1 0.01 0.90 ] #... |XX 1117 - 1118 : [ 1 0.01 0.90 ] #... |XX 1266 - 1267 : [ 1 0.01 0.91 ] #... |XX 1303 - 1304 : [ 1 0.01 0.92 ] #... |XX 1338 - 1339 : [ 1 0.01 0.92 ] #... |XX 1443 - 1444 : [ 1 0.01 0.93 ] #... |XX 1447 - 1448 : [ 1 0.01 0.93 ] #... |XX 1471 - 1472 : [ 1 0.01 0.94 ] #... |XX 1744 - 1745 : [ 1 0.01 0.94 ] #... |XX 1767 - 1768 : [ 1 0.01 0.95 ] #... |XX 1799 - 1800 : [ 1 0.01 0.95 ] #... |XX 2134 - 2135 : [ 1 0.01 0.96 ] #... |XX 2138 - 2139 : [ 1 0.01 0.96 ] #... |XX 2450 - 2451 : [ 1 0.01 0.97 ] #... |XX 2597 - 2598 : [ 1 0.01 0.97 ] #... |XX 3031 - 3032 : [ 1 0.01 0.98 ] #... |XX 3494 - 3495 : [ 1 0.01 0.98 ] #... |XX 3896 - 3897 : [ 1 0.01 0.99 ] #... |XX 4186 - 4187 : [ 1 0.01 0.99 ] #... |XX 9034 - 9035 : [ 1 0.01 1.00 ] ################################################################### Histogram of Contig Size Distribution: ------------------------------------------------------------------- Command: hist contig.grep 5 1000 #Found 189 total values totalling 5508577.0000. <29145.910053 +/- 57592.169543> #Range: [ 200 - 539509 ] #Most likely bin: [ 1000 - 2000 ] 36 counts #Median bin: [ 6000 - 7000 ] 5 counts |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0 - 1000 : [ 25 0.13 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1000 - 2000 : [ 36 0.19 0.32 ] |XXXXXXXXXXXX 2000 - 3000 : [ 11 0.06 0.38 ] |XXXXXXXXXX 3000 - 4000 : [ 9 0.05 0.43 ] |XXXX 4000 - 5000 : [ 4 0.02 0.45 ] |XXXXXX 5000 - 6000 : [ 5 0.03 0.48 ] |XXXXXX 6000 - 7000 : [ 5 0.03 0.50 ] |X 7000 - 8000 : [ 1 0.01 0.51 ] |X 8000 - 9000 : [ 1 0.01 0.51 ] |XX 9000 - 10000 : [ 2 0.01 0.52 ] |X 10000 - 11000 : [ 1 0.01 0.53 ] |XXXXXX 11000 - 12000 : [ 5 0.03 0.56 ] |XXX 12000 - 13000 : [ 3 0.02 0.57 ] |XX 13000 - 14000 : [ 2 0.01 0.58 ] |X 14000 - 15000 : [ 1 0.01 0.59 ] |XXXXXX 15000 - 16000 : [ 5 0.03 0.61 ] |X 16000 - 17000 : [ 1 0.01 0.62 ] |X 17000 - 18000 : [ 1 0.01 0.62 ] |X 18000 - 19000 : [ 1 0.01 0.63 ] #... |XX 21000 - 22000 : [ 2 0.01 0.64 ] |XX 22000 - 23000 : [ 2 0.01 0.65 ] |XXX 23000 - 24000 : [ 3 0.02 0.67 ] |X 24000 - 25000 : [ 1 0.01 0.67 ] |XX 25000 - 26000 : [ 2 0.01 0.68 ] |XXX 26000 - 27000 : [ 3 0.02 0.70 ] |XX 27000 - 28000 : [ 2 0.01 0.71 ] |XXXXXX 28000 - 29000 : [ 5 0.03 0.74 ] #... |XX 30000 - 31000 : [ 2 0.01 0.75 ] |X 31000 - 32000 : [ 1 0.01 0.75 ] #... |X 33000 - 34000 : [ 1 0.01 0.76 ] |X 34000 - 35000 : [ 1 0.01 0.76 ] |XX 35000 - 36000 : [ 2 0.01 0.77 ] |XX 36000 - 37000 : [ 2 0.01 0.78 ] #... |X 38000 - 39000 : [ 1 0.01 0.79 ] |X 39000 - 40000 : [ 1 0.01 0.79 ] |X 40000 - 41000 : [ 1 0.01 0.80 ] |XX 41000 - 42000 : [ 2 0.01 0.81 ] |XX 42000 - 43000 : [ 2 0.01 0.82 ] #... |X 44000 - 45000 : [ 1 0.01 0.83 ] #... |X 46000 - 47000 : [ 1 0.01 0.83 ] #... |XX 50000 - 51000 : [ 2 0.01 0.84 ] #... |X 52000 - 53000 : [ 1 0.01 0.85 ] #... |X 54000 - 55000 : [ 1 0.01 0.85 ] |X 55000 - 56000 : [ 1 0.01 0.86 ] #... |X 57000 - 58000 : [ 1 0.01 0.86 ] #... |X 64000 - 65000 : [ 1 0.01 0.87 ] #... |XX 66000 - 67000 : [ 2 0.01 0.88 ] |XX 67000 - 68000 : [ 2 0.01 0.89 ] #... |X 69000 - 70000 : [ 1 0.01 0.89 ] #... |X 71000 - 72000 : [ 1 0.01 0.90 ] |X 72000 - 73000 : [ 1 0.01 0.90 ] #... |X 77000 - 78000 : [ 1 0.01 0.91 ] #... |X 88000 - 89000 : [ 1 0.01 0.92 ] #... |X 91000 - 92000 : [ 1 0.01 0.92 ] |X 92000 - 93000 : [ 1 0.01 0.93 ] #... |X 96000 - 97000 : [ 1 0.01 0.93 ] #... |X 102000 - 103000 : [ 1 0.01 0.94 ] #... |X 104000 - 105000 : [ 1 0.01 0.94 ] #... |X 109000 - 110000 : [ 1 0.01 0.95 ] |X 110000 - 111000 : [ 1 0.01 0.95 ] #... |XX 125000 - 126000 : [ 2 0.01 0.96 ] #... |X 161000 - 162000 : [ 1 0.01 0.97 ] #... |X 183000 - 184000 : [ 1 0.01 0.97 ] #... |X 190000 - 191000 : [ 1 0.01 0.98 ] #... |X 207000 - 208000 : [ 1 0.01 0.98 ] #... |X 238000 - 239000 : [ 1 0.01 0.99 ] #... |X 290000 - 291000 : [ 1 0.01 0.99 ] #... |X 539000 - 540000 : [ 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 AHZF reads.list > grep.reads.list.AHZF Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZF 4 500 #Found 15224 total values totalling 52185925.0000. <3427.872110 +/- 3253.992841> #Range: [ - 174835 ] #Most likely bin: [ 3000 - 3500 ] 7298 counts #Median bin: [ 3000 - 3500 ] 7298 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 21 0.00 0.00 ] |XX 1000 - 1500 : [ 309 0.02 0.02 ] |XX 1500 - 2000 : [ 333 0.02 0.04 ] |XX 2000 - 2500 : [ 308 0.02 0.06 ] |XXXXXX 2500 - 3000 : [ 1032 0.07 0.13 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 7298 0.48 0.61 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 5376 0.35 0.96 ] |XXX 4000 - 4500 : [ 510 0.03 1.00 ] | 4500 - 5000 : [ 15 0.00 1.00 ] | 5000 - 5500 : [ 1 0.00 1.00 ] #... | 29500 - 30000 : [ 1 0.00 1.00 ] #... | 34500 - 35000 : [ 1 0.00 1.00 ] #... | 66500 - 67000 : [ 1 0.00 1.00 ] #... | 71500 - 72000 : [ 1 0.00 1.00 ] #... | 77000 - 77500 : [ 4 0.00 1.00 ] | 77500 - 78000 : [ 3 0.00 1.00 ] | 78000 - 78500 : [ 5 0.00 1.00 ] #... | 86500 - 87000 : [ 1 0.00 1.00 ] #... | 132000 - 132500 : [ 1 0.00 1.00 ] #... | 167500 - 168000 : [ 1 0.00 1.00 ] #... | 174500 - 175000 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHZG reads.list > grep.reads.list.AHZG Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZG 4 500 #Found 12991 total values totalling 111498786.0000. <8582.771611 +/- 4326.403768> #Range: [ - 152147 ] #Most likely bin: [ 8500 - 9000 ] 2214 counts #Median bin: [ 8500 - 9000 ] 2214 counts | 0 - 500 : [ 1 0.00 0.00 ] | 500 - 1000 : [ 27 0.00 0.00 ] |XXX 1000 - 1500 : [ 164 0.01 0.01 ] |XXX 1500 - 2000 : [ 173 0.01 0.03 ] |XXXX 2000 - 2500 : [ 199 0.02 0.04 ] |XXX 2500 - 3000 : [ 192 0.01 0.06 ] |XXX 3000 - 3500 : [ 183 0.01 0.07 ] |XXX 3500 - 4000 : [ 184 0.01 0.09 ] |XXXX 4000 - 4500 : [ 194 0.01 0.10 ] |XXX 4500 - 5000 : [ 157 0.01 0.11 ] |XXX 5000 - 5500 : [ 166 0.01 0.13 ] |XX 5500 - 6000 : [ 133 0.01 0.14 ] |XX 6000 - 6500 : [ 138 0.01 0.15 ] |XX 6500 - 7000 : [ 118 0.01 0.16 ] |XXXX 7000 - 7500 : [ 199 0.02 0.17 ] |XXXXXXXXX 7500 - 8000 : [ 504 0.04 0.21 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8000 - 8500 : [ 1587 0.12 0.33 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8500 - 9000 : [ 2214 0.17 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9000 - 9500 : [ 2151 0.17 0.67 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 9500 - 10000 : [ 1887 0.15 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXX 10000 - 10500 : [ 1363 0.10 0.92 ] |XXXXXXXXXXXXX 10500 - 11000 : [ 704 0.05 0.97 ] |XXXXX 11000 - 11500 : [ 268 0.02 0.99 ] |X 11500 - 12000 : [ 44 0.00 1.00 ] | 12000 - 12500 : [ 5 0.00 1.00 ] #... | 15000 - 15500 : [ 1 0.00 1.00 ] #... | 17500 - 18000 : [ 2 0.00 1.00 ] #... | 20000 - 20500 : [ 1 0.00 1.00 ] #... | 26000 - 26500 : [ 1 0.00 1.00 ] #... | 37500 - 38000 : [ 1 0.00 1.00 ] #... | 43500 - 44000 : [ 1 0.00 1.00 ] #... | 51000 - 51500 : [ 1 0.00 1.00 ] #... | 67500 - 68000 : [ 1 0.00 1.00 ] #... | 79500 - 80000 : [ 1 0.00 1.00 ] #... | 82000 - 82500 : [ 1 0.00 1.00 ] | 82500 - 83000 : [ 4 0.00 1.00 ] | 83000 - 83500 : [ 5 0.00 1.00 ] | 83500 - 84000 : [ 4 0.00 1.00 ] | 84000 - 84500 : [ 5 0.00 1.00 ] | 84500 - 85000 : [ 3 0.00 1.00 ] | 85000 - 85500 : [ 1 0.00 1.00 ] | 85500 - 86000 : [ 1 0.00 1.00 ] #... | 94000 - 94500 : [ 1 0.00 1.00 ] #... | 152000 - 152500 : [ 1 0.00 1.00 ] Command: /usr/xpg4/bin/grep AHZH reads.list > grep.reads.list.AHZH Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AHZH 4 500 #Found 1091 total values totalling 44038750.0000. <40365.490376 +/- 11415.579319> #Range: [ - 157926 ] #Most likely bin: [ 36500 - 37000 ] 59 counts #Median bin: [ 39000 - 39500 ] 43 counts |X 0 - 500 : [ 1 0.00 0.00 ] #... |X 3500 - 4000 : [ 1 0.00 0.00 ] #... |X 15500 - 16000 : [ 1 0.00 0.00 ] #... |X 19000 - 19500 : [ 1 0.00 0.00 ] #... |X 27500 - 28000 : [ 1 0.00 0.00 ] |X 28000 - 28500 : [ 1 0.00 0.01 ] #... |XX 29500 - 30000 : [ 3 0.00 0.01 ] |XXXX 30000 - 30500 : [ 6 0.01 0.01 ] |XXX 30500 - 31000 : [ 4 0.00 0.02 ] |XXXXX 31000 - 31500 : [ 8 0.01 0.02 ] |XXXXXX 31500 - 32000 : [ 9 0.01 0.03 ] |XXXXXXXXXXXXX 32000 - 32500 : [ 19 0.02 0.05 ] |XXXXXXXXXXXXXXXX 32500 - 33000 : [ 23 0.02 0.07 ] |XXXXXXXXXXXXXX 33000 - 33500 : [ 21 0.02 0.09 ] |XXXXXXXXXXXXXXXXXX 33500 - 34000 : [ 27 0.02 0.12 ] |XXXXXXXXXXXXXXXXX 34000 - 34500 : [ 25 0.02 0.14 ] |XXXXXXXXXXXXXXXXXX 34500 - 35000 : [ 27 0.02 0.16 ] |XXXXXXXXXXXXXXXXXXXXXX 35000 - 35500 : [ 32 0.03 0.19 ] |XXXXXXXXXXXXXXXXXXXXXX 35500 - 36000 : [ 33 0.03 0.22 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 36000 - 36500 : [ 38 0.03 0.26 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 36500 - 37000 : [ 59 0.05 0.31 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37000 - 37500 : [ 53 0.05 0.36 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 37500 - 38000 : [ 49 0.04 0.41 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38000 - 38500 : [ 56 0.05 0.46 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 38500 - 39000 : [ 44 0.04 0.50 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39000 - 39500 : [ 43 0.04 0.54 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 39500 - 40000 : [ 45 0.04 0.58 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 40000 - 40500 : [ 53 0.05 0.63 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 40500 - 41000 : [ 38 0.03 0.66 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 41000 - 41500 : [ 40 0.04 0.70 ] |XXXXXXXXXXXXXXXXXXXXXXXXXX 41500 - 42000 : [ 39 0.04 0.73 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 42000 - 42500 : [ 40 0.04 0.77 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXXX 42500 - 43000 : [ 42 0.04 0.81 ] |XXXXXXXXXXXXXXXXXXXXXXXXXXX 43000 - 43500 : [ 40 0.04 0.85 ] |XXXXXXXXXXXXXXXXXX 43500 - 44000 : [ 27 0.02 0.87 ] |XXXXXXXXXXXXXXXXXXXXXX 44000 - 44500 : [ 33 0.03 0.90 ] |XXXXXXXXXXXXXXXXXXXXX 44500 - 45000 : [ 31 0.03 0.93 ] |XXXXXXXXXXXXXXXX 45000 - 45500 : [ 23 0.02 0.95 ] |XXXXXXXXXX 45500 - 46000 : [ 15 0.01 0.96 ] |XXXXX 46000 - 46500 : [ 8 0.01 0.97 ] |XXXXX 46500 - 47000 : [ 7 0.01 0.98 ] |XXX 47000 - 47500 : [ 4 0.00 0.98 ] #... |X 106500 - 107000 : [ 1 0.00 0.98 ] #... |X 109000 - 109500 : [ 1 0.00 0.98 ] |X 109500 - 110000 : [ 1 0.00 0.98 ] |X 110000 - 110500 : [ 1 0.00 0.98 ] |X 110500 - 111000 : [ 1 0.00 0.99 ] #... |X 111500 - 112000 : [ 1 0.00 0.99 ] |XX 112000 - 112500 : [ 3 0.00 0.99 ] #... |X 113000 - 113500 : [ 2 0.00 0.99 ] |X 113500 - 114000 : [ 2 0.00 0.99 ] #... |X 115500 - 116000 : [ 2 0.00 0.99 ] |X 116000 - 116500 : [ 2 0.00 1.00 ] #... |X 117000 - 117500 : [ 1 0.00 1.00 ] |X 117500 - 118000 : [ 1 0.00 1.00 ] |X 118000 - 118500 : [ 1 0.00 1.00 ] #... |X 157500 - 158000 : [ 1 0.00 1.00 ] ################################################################### Estimated Assembled Average Insert Sizes Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out ------------------------------------------------------------------- # AHZH 38814 +- 4386 (n=524) # AHZF 3172 +- 790 (n=7892) # AHZG 8159 +- 2537 (n=6646) ################################################################### 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 612.236171 bp, 82561 reads, genome size 6216108 bp Command: idealAssembly 6216108 82561 612.236171 ------------------------------------------------------------------- Genome = 6216108 bases Nreads = 82561 readLength = 612.236171 Depth = 8.13 N_contigs = N_gaps = 24 mean gap size = 74 bases mean contig size = 3400 reads (~ 256004 bases) %cover = 99.97 %singlet = 0.00 assembly size = 6214275 bases Contig size distribution: ------------------------- N50 (analytic): About half the reads will be in 5 contigs containing at least 5706 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: