# This file is a tab-delimited table of read counts and accession numbers for the samples S&R NPD mutant experiment conducted in winter 2018 with the 68 strain community # # Column names # pool : sample name # raw_n_pairs : number of read pairs in the raw data # trimmed_n_pairs : number of read pairs left after quality trimming # aln_n_reads : number of reads (not pairs!) that aligned to USDA1106 (reference) # marked_dups : number of reads marked as PCR duplicates by samtools # dup_rate : proportion of reads that were marked as duplicates # aln_rate : proportion of trimmed reads that aligned to the reference # biosample_accession : BioSample for this pool # sra_accession : SRA accession for this pool # description : Brief description of host genotype, community, and other conditions # pool raw_n_pairs trimmed_n_pairs trimmed_rate aln_n_reads marked_dups dup_rate aln_rate biosample_accession sra_accession description C68_Gm12-7_D1 5646645 4904952 0.868648906 7562664 274477 0.036293692 0.770921306 SAMN10182565 SRR7974412 "M. truncatula R108 Gm12-7 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm12-7_D2 4414339 3827197 0.866992091 6099820 196596 0.032229804 0.796904366 SAMN10182566 SRR7974409 "M. truncatula R108 Gm12-7 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm12-7_D3 5884051 5044820 0.857371902 8000376 306682 0.038333448 0.792929777 SAMN10182567 SRR7974410 "M. truncatula R108 Gm12-7 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm20-2_D1 6281162 5444258 0.866759686 8977561 351725 0.039178236 0.824498123 SAMN10182568 SRR7974415 "M. truncatula R108 Gm20-2 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm20-2_D2 4924353 4247203 0.862489549 7045416 237539 0.033715397 0.829418325 SAMN10182569 SRR7974416 "M. truncatula R108 Gm20-2 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm20-2_D3 5040587 4339597 0.86093088 7375900 263766 0.035760517 0.849836978 SAMN10182570 SRR7974413 "M. truncatula R108 Gm20-2 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm26-1_D1 5339560 4581963 0.858116212 7614888 270550 0.035529085 0.830963498 SAMN10182571 SRR7974414 "M. truncatula R108 Gm26-1 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm26-1_D2 4784291 4099589 0.856885378 6401488 203285 0.031755898 0.780747533 SAMN10182572 SRR7974407 "M. truncatula R108 Gm26-1 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm26-1_D3 4777626 4118525 0.862044245 6856731 232540 0.03391412 0.832425565 SAMN10182573 SRR7974408 "M. truncatula R108 Gm26-1 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm8-5_D1 3674139 3069191 0.835349724 5155415 138361 0.026837995 0.839865456 SAMN10182574 SRR7974423 "M. truncatula R108 Gm8-5 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm8-5_D2 4852169 4156440 0.856614846 6958224 222814 0.032021677 0.837041314 SAMN10182575 SRR7974422 "M. truncatula R108 Gm8-5 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_Gm8-5_D3 5791660 4980580 0.859957249 8407312 317806 0.037801143 0.844009332 SAMN10182576 SRR7974425 "M. truncatula R108 Gm8-5 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" C68_initial_1 3580266 3162810 0.883400842 5371900 182262 0.033928778 0.849229008 SAMN09838915 SRR7699692 "Initial synthetic community, 68 strain mixture" C68_initial_2 2832586 2462051 0.869188438 4182024 127937 0.030592125 0.849296785 SAMN09838916 SRR7699691 "Initial synthetic community, 68 strain mixture" C68_initial_5 4300005 3822137 0.888868036 6489074 244427 0.03766747 0.848880351 SAMN09838917 SRR7699694 "Initial synthetic community, 68 strain mixture" C68_initial_8 2556482 2223462 0.86973505 3780160 112990 0.029890269 0.850061751 SAMN09838918 SRR7699693 "Initial synthetic community, 68 strain mixture" HM340_D1 4725055 4087399 0.86504792 6170467 218607 0.035427951 0.754815838 SAMN09838964 SRR7699615 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" HM340_D2 3771299 3362631 0.891637338 5297458 179485 0.033881345 0.787695409 SAMN09838965 SRR7699612 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" HM340_D3 4219027 3726774 0.883325468 4943515 174465 0.03529169 0.663243196 SAMN09838966 SRR7699613 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" HM340_U1 5057327 4488728 0.887569263 4679967 169637 0.036247478 0.521302137 SAMN09838967 SRR7699620 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment" HM340_U2 6396154 5689665 0.889544717 5888415 292172 0.049618106 0.517465879 SAMN09838968 SRR7699621 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment" HM340_U3 7076612 6041128 0.853675177 7074174 296213 0.04187245 0.585501085 SAMN09838969 SRR7699577 "M. truncatula R108 nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment" MPC12_D1 4084497 3656843 0.895298246 6102742 209390 0.034310807 0.834427674 SAMN09839006 SRR7699660 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" MPC12_D2 5810885 5226624 0.899454042 8635864 378899 0.043875054 0.826141693 SAMN09839007 SRR7699655 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" MPC12_D3 3500760 3138220 0.89643963 5409951 173690 0.032105651 0.861945785 SAMN09839008 SRR7699656 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, differentiated bacteria, mutant experiment" MPC12_U1 5325688 4784625 0.898405051 8249948 353916 0.042899179 0.862131097 SAMN09839009 SRR7699633 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment" MPC12_U2 5545294 4829010 0.870830293 8061268 431733 0.053556463 0.834670875 SAMN09839010 SRR7699632 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment" MPC12_U3 3704739 3321878 0.896656418 5806020 193891 0.033394821 0.873906266 SAMN09839011 SRR7699634 "M. truncatula R108 5 npd gene knockout nodule community after inoculation with 68 strain mixture, undifferentiated bacteria, mutant experiment"