{"text_format":"3","workbook":"xls","n_sheets":1,"sheets":["Report_Samples"],"read":"whole","date_system":"1900","formulas":"cached_only"}

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["Final Alignment Report"]
["Bismark report (version: v0.19.1)"]
["Bismark was run with Bowtie 2 against the bisulfite genome of /mnt/data2/lbcb/reference/grch38/ with the specified options: -q -L 19 --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500"]
["Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)"]
[]
["Final Alignment report","CT2","CT3","CT4","CT5","CT6","CT7","EC_1","EC_2","LTNP_1","LTNP_2","LTNP_3","LTNP_4","LTNP_5","LTNP_6","VR_1","VR_2","VR_3","VR_4","VR_5","VR_6","VR_7","VF_1","VF_2","VF_3","VF_4","VF_5","VF_6","VF_7"]
["======================"]
["Sequence pairs analysed in total:",75795648,94399443,80086748,79415613,88463081,76209574,81762748,73691929,42774664,70214120,43055432,72109959,94827760,92990225,81180747,41870343,103526872,87854167,78420054,70855150,76417721,84127148,82780569,90262797,88034488,91088176,70670117,84413161]
["Number of paired-end alignments with a unique best hit:",65826787,81818555,69617394,68958488,76659216,66339147,64266827,57192457,34250475,58042939,35339181,59296536,75585740,72425283,69746116,31684519,89927247,70695532,63460432,56459199,66271447,72372892,71713969,78226433,76334313,70450906,56463752,73318177]
["Mapping efficiency:",{"v":0.868,"d":"86.80%"},{"v":0.867,"d":"86.70%"},{"v":0.869,"d":"86.90%"},{"v":0.868,"d":"86.80%"},{"v":0.867,"d":"86.70%"},{"v":0.87,"d":"87.00%"},{"v":0.786,"d":"78.60%"},{"v":0.776,"d":"77.60%"},{"v":0.801,"d":"80.10%"},{"v":0.827,"d":"82.70%"},{"v":0.821,"d":"82.10%"},{"v":0.822,"d":"82.20%"},{"v":0.797,"d":"79.70%"},{"v":0.779,"d":"77.90%"},{"v":0.859,"d":"85.90%"},{"v":0.757,"d":"75.70%"},{"v":0.869,"d":"86.90%"},{"v":0.805,"d":"80.50%"},{"v":0.809,"d":"80.90%"},{"v":0.797,"d":"79.70%"},{"v":0.867,"d":"86.70%"},{"v":0.86,"d":"86.00%"},{"v":0.866,"d":"86.60%"},{"v":0.867,"d":"86.70%"},{"v":0.867,"d":"86.70%"},{"v":0.773,"d":"77.30%"},{"v":0.799,"d":"79.90%"},{"v":0.869,"d":"86.90%"}]
["Sequence pairs with no alignments under any condition:",8526397,10693283,8860496,8932797,10053563,8339231,16411102,15516602,7914578,11200222,7100052,11825089,17949451,19279993,9837977,9610222,11529197,15992534,13847491,13352086,8664017,10170174,9393978,10196999,10076646,19394597,13181043,9365709]
["Sequence pairs did not map uniquely:",1442464,1887605,1608858,1524328,1750302,1531196,1084819,982870,609611,970959,616199,988334,1292569,1284949,1596654,575602,2070428,1166101,1112131,1043865,1482257,1584082,1672622,1839365,1623529,1242673,1025322,1729275]
["Sequence pairs which were discarded because genomic sequence could not be extracted:",1,8,17,0,7,1,11,11,2,0,0,1,1,6,3,0,10,2,0,3,9,23,16,31,1,5,1,7]
[]
["Number of sequence pairs with unique best (first) alignment came from the bowtie output:"]
["CT/GA/CT: ((converted) top strand)",2647860,3247805,2748225,2738291,3090745,2486962,1605272,1370418,851408,1513041,868434,1474567,1899399,1762730,2772864,717003,3514122,1678804,1514046,1336711,2576207,2794840,2845191,3109504,3045124,1722782,1429738,2852909]
["GA/CT/CT: (complementary to (converted) top strand)",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["GA/CT/GA: (complementary to (converted) bottom strand)",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["CT/GA/GA: ((converted) bottom strand)",63178926,78570742,66869152,66220197,73568464,63852184,62661544,55822028,33399065,56529898,34470747,57821968,73686340,70662547,66973249,30967516,86413115,69016726,61946386,55122485,63695231,69578029,68868762,75116898,73289188,68728119,55034013,70465261]
[]
["Number of alignments to (merely theoretical) complementary strands being rejected in total:",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
[]
["Final Cytosine Methylation Report"]
["================================="]
["Total number of C's analysed:",3071819132,3861403240,3269603058,3226228436,3589876885,3125598308,3051539312,2719907233,1656957075,2774878057,1708597440,2847437440,3620798240,3505599058,3273037197,1537019575,4239664378,3387253340,3056184813,2765981672,3121575526,3399277483,3364666647,3699260122,3581437898,3413861993,2727916405,3456846858]
[]
["Total methylated C's in CpG context:",172899902,220720973,191478380,183056978,205776841,179135587,165672372,149393986,94730600,154506696,90661148,156334938,195827152,188377650,185411753,87997760,242868791,185911996,169742526,158132033,178330545,199348397,193002292,212776880,207305488,192680939,159699761,205091081]
["Total methylated C's in CHG context:",7986201,10096309,9373607,8720357,10508799,8060670,10880259,9992360,3739178,6398203,3751823,10377465,14064609,12967456,8492913,3385897,11010321,7131612,6099739,7494647,8066161,15061523,14439248,14348853,15966744,9509052,7383616,15301702]
["Total methylated C's in CHH context:",19671955,24460860,22508657,21099438,25251268,19194718,26849342,24544245,8796759,15195690,9006857,25300549,34594615,31503193,20457371,7713208,26487232,17214289,14324310,17595218,19337388,35799744,34285750,33739622,37923337,22619755,16814670,36004655]
["Total methylated C's in Unknown context:",20599,25318,21321,20561,24059,20108,47780,52899,34772,34815,22852,40355,48537,64832,20813,41074,28886,58651,54765,63046,20422,25993,25632,27001,25404,90010,53693,26313]
[]
[]
["Total unmethylated C's in CpG context:",166184196,220182206,184041479,180752738,205670307,182974158,163878273,145784674,99556356,161527478,103726215,158047684,199712279,201347986,184958209,101176913,241911324,196156815,187554258,169139218,177210210,187412469,190503417,215886083,201252392,198001249,172694241,194312800]
["Total unmethylated C's in CHG context:",752990812,953190688,810601877,796927403,890685180,777177129,737392307,656452129,412610629,686854574,419565786,690120776,873590427,849789188,809116521,386821191,1050783242,829508472,757260087,683246336,772516910,835654448,828624083,916520364,880995689,838389350,685876556,854327412]
["Total unmethylated C's in CHH context:",1952086066,2432752204,2051599058,2035671522,2251984490,1959056046,1946866759,1733739839,1037523553,1750395416,1081885611,1807256028,2303009158,2221613585,2064600430,949924606,2666603468,2151330156,1921203893,1730374220,1966114312,2126000902,2103811857,2305988320,2237994248,2152661648,1685447561,2151809208]
["Total unmethylated C's in Unknown context:",2383246,2953458,2493086,2451664,2673913,2378588,1971567,1806805,1127793,1813529,1092105,1839330,2360957,2301555,2500248,1140815,3250892,2427331,2227500,2013851,2401660,2541980,2556114,2821880,2665693,2390766,1856307,2590206]
[]
[]
["C methylated in CpG context:",{"v":0.51,"d":"51.00%"},{"v":0.501,"d":"50.10%"},{"v":0.51,"d":"51.00%"},{"v":0.503,"d":"50.30%"},{"v":0.5,"d":"50.00%"},{"v":0.495,"d":"49.50%"},{"v":0.503,"d":"50.30%"},{"v":0.506,"d":"50.60%"},{"v":0.488,"d":"48.80%"},{"v":0.489,"d":"48.90%"},{"v":0.466,"d":"46.60%"},{"v":0.497,"d":"49.70%"},{"v":0.495,"d":"49.50%"},{"v":0.483,"d":"48.30%"},{"v":0.501,"d":"50.10%"},{"v":0.465,"d":"46.50%"},{"v":0.501,"d":"50.10%"},{"v":0.487,"d":"48.70%"},{"v":0.475,"d":"47.50%"},{"v":0.483,"d":"48.30%"},{"v":0.502,"d":"50.20%"},{"v":0.515,"d":"51.50%"},{"v":0.503,"d":"50.30%"},{"v":0.496,"d":"49.60%"},{"v":0.507,"d":"50.70%"},{"v":0.493,"d":"49.30%"},{"v":0.48,"d":"48.00%"},{"v":0.513,"d":"51.30%"}]
["C methylated in CHG context:",{"v":0.01,"d":"1.00%"},{"v":0.01,"d":"1.00%"},{"v":0.011,"d":"1.10%"},{"v":0.011,"d":"1.10%"},{"v":0.012,"d":"1.20%"},{"v":0.01,"d":"1.00%"},{"v":0.015,"d":"1.50%"},{"v":0.015,"d":"1.50%"},{"v":0.009,"d":"0.90%"},{"v":0.009,"d":"0.90%"},{"v":0.009,"d":"0.90%"},{"v":0.015,"d":"1.50%"},{"v":0.016,"d":"1.60%"},{"v":0.015,"d":"1.50%"},{"v":0.01,"d":"1.00%"},{"v":0.009,"d":"0.90%"},{"v":0.01,"d":"1.00%"},{"v":0.009,"d":"0.90%"},{"v":0.008,"d":"0.80%"},{"v":0.011,"d":"1.10%"},{"v":0.01,"d":"1.00%"},{"v":0.018,"d":"1.80%"},{"v":0.017,"d":"1.70%"},{"v":0.015,"d":"1.50%"},{"v":0.018,"d":"1.80%"},{"v":0.011,"d":"1.10%"},{"v":0.011,"d":"1.10%"},{"v":0.018,"d":"1.80%"}]
["C methylated in CHH context:",{"v":0.01,"d":"1.00%"},{"v":0.01,"d":"1.00%"},{"v":0.011,"d":"1.10%"},{"v":0.01,"d":"1.00%"},{"v":0.011,"d":"1.10%"},{"v":0.01,"d":"1.00%"},{"v":0.014,"d":"1.40%"},{"v":0.014,"d":"1.40%"},{"v":0.008,"d":"0.80%"},{"v":0.009,"d":"0.90%"},{"v":0.008,"d":"0.80%"},{"v":0.014,"d":"1.40%"},{"v":0.015,"d":"1.50%"},{"v":0.014,"d":"1.40%"},{"v":0.01,"d":"1.00%"},{"v":0.008,"d":"0.80%"},{"v":0.01,"d":"1.00%"},{"v":0.008,"d":"0.80%"},{"v":0.007,"d":"0.70%"},{"v":0.01,"d":"1.00%"},{"v":0.01,"d":"1.00%"},{"v":0.017,"d":"1.70%"},{"v":0.016,"d":"1.60%"},{"v":0.014,"d":"1.40%"},{"v":0.017,"d":"1.70%"},{"v":0.01,"d":"1.00%"},{"v":0.01,"d":"1.00%"},{"v":0.016,"d":"1.60%"}]
["C methylated in unknown context (CN or CHN):",{"v":0.009,"d":"0.90%"},{"v":0.008,"d":"0.80%"},{"v":0.008,"d":"0.80%"},{"v":0.008,"d":"0.80%"},{"v":0.009,"d":"0.90%"},{"v":0.008,"d":"0.80%"},{"v":0.024,"d":"2.40%"},{"v":0.028,"d":"2.80%"},{"v":0.03,"d":"3.00%"},{"v":0.019,"d":"1.90%"},{"v":0.02,"d":"2.00%"},{"v":0.021,"d":"2.10%"},{"v":0.02,"d":"2.00%"},{"v":0.027,"d":"2.70%"},{"v":0.008,"d":"0.80%"},{"v":0.035,"d":"3.50%"},{"v":0.009,"d":"0.90%"},{"v":0.024,"d":"2.40%"},{"v":0.024,"d":"2.40%"},{"v":0.03,"d":"3.00%"},{"v":0.008,"d":"0.80%"},{"v":0.01,"d":"1.00%"},{"v":0.01,"d":"1.00%"},{"v":0.009,"d":"0.90%"},{"v":0.009,"d":"0.90%"},{"v":0.036,"d":"3.60%"},{"v":0.028,"d":"2.80%"},{"v":0.01,"d":"1.00%"}]
[]
["Conversion Statistics: average conversion rate ",99.043832901102,99.037279515143,98.954721342959,99.010174928565,98.927438250821,99.063889894812,98.65555378796,98.616711046899,99.182369042131,99.148467262897,99.188329955335,98.624786157181,98.531326292271,98.610180692178,99.052750627165,99.217818435513,99.051931680569,99.211948856022,99.274760445123,99.004262349995,99.063128359361,98.38110660366,98.432394364545,98.596524785308,98.380813732347,98.959225221223,99.030500834525,98.39878925749]