Built data using BWA to estimate cDNA abundance in sequenced maize lines from Jiao et al (2012)
Get raw data from tab delimited table.
setwd("/Users/Sid/Projects/")
x = read.table("Jiao_cDNA_abun.stat", header = T)
print(x)
## Line Accession Total_Reads Reads_Mapped
## 1 CAU06_zong31 SRR448305.sra 70376782 11751662
## 2 CAU07_D340 SRR448306.sra 66581692 11368518
## 3 CAU08_H127 SRR448307.sra 62498258 10884480
## 4 CAU10_yu87-1 SRR448310.sra 73922520 11709106
## 5 CAU100_shen5005 SRR448311.sra 12789712 2223822
## 6 CAU103_807D SRR448312.sra 16378630 3234612
## 7 CAU105_1145 SRR448313.sra 24844498 4963000
## 8 CAU105_1145 SRR448314.sra 30732844 6303284
## 9 CAU107_D15 SRR448315.sra 53884742 11162194
## 10 CAU11_longkang11 SRR448316.sra 71303880 10754688
## 11 CAU112_S22 SRR448317.sra 27992552 5631410
## 12 CAU114_Q1261 SRR448318.sra 43688370 9250550
## 13 CAU115_ye52106 SRR448319.sra 50694684 10155080
## 14 CAU116_1205A SRR448320.sra 54989120 11482296
## 15 CAU118_K12 SRR448321.sra 66325306 15186432
## 16 CAU12_danhuang02 SRR448322.sra 70550372 10938700
## 17 CAU120_xing230 SRR448324.sra 37539234 7278254
## 18 CAU125_K22 SRR448325.sra 27708000 5440232
## 19 CAU125_K22 SRR448326.sra 30869386 6167000
## 20 CAU129_P007 SRR448328.sra 24669700 5800526
## 21 CAU131_Yd6 SRR448332.sra 39565846 8794128
## 22 CAU132_IA5125 SRR448333.sra 35050790 7060990
## 23 CAU133_liao2202 SRR448334.sra 11549652 2458770
## 24 CAU134_dai6 SRR448336.sra 31403208 6243232
## 25 CAU137_W499 SRR448337.sra 34527392 7301770
## 26 CAU14_shen137 SRR448338.sra 47654598 7552766
## 27 CAU140_XOP2 SRR448340.sra 44393734 9391928
## 28 CAU142_D20 SRR448341.sra 38222516 8206698
## 29 CAU143_hai1134 SRR448342.sra 43072954 8841202
## 30 CAU144_yu374 SRR448343.sra 32366838 6705910
## 31 CAU146_dan9064 SRR448344.sra 49559620 10763872
## 32 CAU147_niu2-1 SRR448345.sra 13595750 3157190
## 33 CAU148_suwan1611 SRR448346.sra 44226768 11195502
## 34 CAU149_R017 SRR448347.sra 34152220 6526300
## 35 CAU15_zheng22 SRR448348.sra 29831374 4275576
## 36 CAU151_shen977 SRR448349.sra 20031072 4186144
## 37 CAU156_huangchangb SRR448350.sra 11536754 2907194
## 38 CAU16_lv28 SRR448351.sra 57801942 8678496
## 39 CAU164_K10 SRR448352.sra 19411754 3579474
## 40 CAU165_ye5237 SRR448353.sra 24808102 4852162
## 41 CAU166_zheng32 SRR448354.sra 52716414 9729032
## 42 CAU17_huangC SRR448355.sra 57657996 9121656
## 43 CAU173_P167 SRR448356.sra 28778874 5424846
## 44 CAU174_R31 SRR448357.sra 23687032 4552484
## 45 CAU178_changK SRR448358.sra 95390126 20486192
## 46 CAU18_P138 SRR448359.sra 20635296 3177444
## 47 CAU180_M131-5 SRR448360.sra 61963408 14425670
## 48 CAU19_zi330 SRR448361.sra 20231930 2210504
## 49 CAU191_hai014 SRR448362.sra 29611676 5474032
## 50 CAU192_ji444 SRR448363.sra 32494330 6051942
## 51 CAU193_ben7884 SRR448364.sra 26919086 5189638
## 52 CAU194_huangyesi3 SRR448365.sra 54939872 9975014
## 53 CAU195_zaC546 SRR448366.sra 26994450 4421520
## 54 CAU197_4F1 SRR448367.sra 54271394 10270554
## 55 CAU198_wenhuang31413 SRR448368.sra 40677216 7323818
## 56 CAU199_ye515 SRR448369.sra 28517790 5336274
## 57 CAU20_huangzaosi SRR448370.sra 191447520 25081664
## 58 CAU200_hu803 SRR448371.sra 30975942 6052586
## 59 CAU201_tian77 SRR448372.sra 25215182 4673270
## 60 CAU202_ye488 SRR448373.sra 34138340 6385208
## 61 CAU203_chang72 SRR448388.sra 35114958 6790090
## 62 CAU207_3H2 SRR448389.sra 30523744 5385740
## 63 CAU208_cheng698-3 SRR448390.sra 45368756 8679264
## 64 CAU21_tie7922 SRR448391.sra 34680814 5360994
## 65 CAU210_su75 SRR448392.sra 22744484 4360312
## 66 CAU211_Beck SRR448393.sra 24646984 4602166
## 67 CAU215_P136 SRR448394.sra 21909330 4316120
## 68 CAU217_dan9046 SRR448395.sra 111018246 21607698
## 69 CAU224_W64a SRR448397.sra 28359710 5473788
## 70 CAU225_A554 SRR448398.sra 22630300 4665756
## 71 CAU229_xun92-8 SRR448399.sra 25377004 4925178
## 72 CAU234_H21 SRR448400.sra 890232 172368
## 73 CAU234_H21 SRR448401.sra 16093792 2341032
## 74 CAU235_shuang741 SRR448444.sra 561342 97544
## 75 CAU235_shuang741 SRR448445.sra 15610706 2321648
## 76 CAU236_200B SRR448446.sra 1097720 185278
## 77 CAU236_200B SRR448447.sra 30295046 4799286
## 78 CAU237_chong72 SRR448490.sra 772862 142830
## 79 CAU237_chong72 SRR448491.sra 15931402 2217132
## 80 CAU238_Pa91 SRR448492.sra 1333286 254100
## 81 CAU238_Pa91 SRR448493.sra 17120196 2495424
## 82 CAU239_yu537A SRR448494.sra 1137230 213570
## 83 CAU239_yu537A SRR448495.sra 17234410 2678516
## 84 CAU24_9058 SRR448496.sra 31348844 5085218
## 85 CAU242_dan3115 SRR448497.sra 38621670 7267130
## 86 CAU244_zhonghuang64 SRR448522.sra 37965758 6984874
## 87 CAU247_dong327 SRR448565.sra 20027474 3752498
## 88 CAU248_698-3 SRR448566.sra 40819584 8407974
## 89 CAU248_698-3 SRR448567.sra 23514374 5004834
## 90 CAU25_ji853 SRR448568.sra 32946090 5387742
## 91 CAU251_N138 SRR448569.sra 28435818 5638746
## 92 CAU251_N138 SRR448570.sra 27559438 5666414
## 93 CAU254_DM07 SRR448571.sra 15908380 3210470
## 94 CAU254_DM07 SRR448572.sra 28686284 6013988
## 95 CAU256_B100 SRR448573.sra 15007344 3602100
## 96 CAU257_B98 SRR448576.sra 60430820 13069752
## 97 CAU261_lian87 SRR448577.sra 18835652 3785498
## 98 CAU264_L-1 SRR448579.sra 23836414 5077832
## 99 CAU271_changD SRR448584.sra 40275098 8365370
## 100 CAU273_M101 SRR448592.sra 30015712 6664942
## 101 CAU275_B394 SRR448595.sra 24324930 5423104
## 102 CAU282_R25 SRR448597.sra 20094396 4162630
## 103 CAU282_R25 SRR448599.sra 20459638 4316656
## 104 CAU283_chengzi108 SRR448600.sra 45409046 9737886
## 105 CAU289_ye107 SRR448601.sra 12314076 2229832
## 106 CAU289_ye107 SRR448603.sra 37242348 6889776
## 107 CAU29_Maxa SRR448604.sra 23834972 3878808
## 108 CAU290_jiutai1 SRR448605.sra 35807010 7149786
## 109 CAU294_hai9-21 SRR448624.sra 24543810 5083818
## 110 CAU295_ji533 SRR448625.sra 16686880 3254602
## 111 CAU297_ye832 SRR448626.sra 11611344 2265496
## 112 CAU302_B76 SRR448627.sra 7843558 1523242
## 113 CAU302_B76 SRR448628.sra 15215268 2305474
## 114 CAU303_NC268 SRR448629.sra 10299558 2091624
## 115 CAU303_NC268 SRR448630.sra 19503648 3983990
## 116 CAU306_Sg1533 SRR448631.sra 6565500 1176450
## 117 CAU306_Sg1533 SRR448632.sra 13854582 2080536
## 118 CAU310_7327 SRR448635.sra 26394368 4938050
## 119 CAU316_bao3040 SRR448636.sra 28479496 5103702
## 120 CAU320_Lx9801 SRR448637.sra 1355522 246194
## 121 CAU320_Lx9801 SRR448638.sra 14766834 2216146
## 122 CAU326_shen135 SRR448639.sra 72810158 16662060
## 123 CAU332_baihe43 SRR448640.sra 18272456 3290242
## 124 CAU34_nan21-3 SRR448641.sra 33473400 5738410
## 125 CAU345_jiu138-5 SRR448642.sra 49445552 9782372
## 126 CAU347_ning55 SRR448643.sra 29818296 5826008
## 127 CAU350_han21 SRR448644.sra 28387428 5248956
## 128 CAU355_huotanghuang SRR448645.sra 34007834 6341528
## 129 CAU357_yu82 SRR448646.sra 24395098 4807752
## 130 CAU359_CN165 SRR448647.sra 20832640 3958900
## 131 CAU361_fu8701 SRR448648.sra 20832656 3876936
## 132 CAU362_De811 SRR448649.sra 15560462 3300838
## 133 CAU365_shan89 SRR448651.sra 23009056 4444022
## 134 CAU366_A679 SRR448652.sra 20209040 4313716
## 135 CAU367_Va26 SRR448653.sra 18880484 3555156
## 136 CAU370_E28 SRR448654.sra 15504016 3092554
## 137 CAU372_zhongyin15 SRR448655.sra 10697678 2197432
## 138 CAU372_zhongyin15 SRR448656.sra 16431762 3392016
## 139 CAU375_zong3 SRR448657.sra 22205934 3568896
## 140 CAU382_FC-13 SRR448658.sra 22939622 4386848
## 141 CAU384_ji63 SRR448659.sra 1265998 234346
## 142 CAU384_ji63 SRR448660.sra 19508948 3424076
## 143 CAU385_ji434 SRR448661.sra 34144328 5711746
## 144 CAU386_ji4112 SRR448662.sra 1288462 222530
## 145 CAU386_ji4112 SRR448663.sra 25554288 4436304
## 146 CAU389_qi205 SRR448664.sra 14504146 2837000
## 147 CAU40_B68 SRR448665.sra 13707906 2800868
## 148 CAU400_P25 SRR448666.sra 32540712 6885722
## 149 CAU401_R98 SRR448667.sra 26806642 5992190
## 150 CAU402_qi319 SRR448668.sra 9226006 1894714
## 151 CAU402_qi319 SRR448669.sra 18018544 3686480
## 152 CAU405_huo17 SRR448670.sra 28925422 5379644
## 153 CAU409_huangyesi SRR448671.sra 37270516 8593738
## 154 CAU411_shen142 SRR448672.sra 21836150 5083134
## 155 CAU413_siyi SRR448673.sra 19122334 4543392
## 156 CAU416_xun971 SRR448674.sra 15537756 3497108
## 157 CAU420_Mo24W SRR448676.sra 33310432 7167320
## 158 CAU422_W182bn SRR448678.sra 26094066 5227134
## 159 CAU423_W153R SRR448679.sra 9825844 2035962
## 160 CAU423_W153R SRR448680.sra 16908704 3519328
## 161 CAU425_HP301 SRR448682.sra 11121326 2237822
## 162 CAU425_HP301 SRR448684.sra 13907546 2856904
## 163 CAU426_H84 SRR448685.sra 17247522 3647308
## 164 CAU429_tangsipingtou SRR448693.sra 38921910 8992336
## 165 CAU434_cheng18 SRR448742.sra 49503480 10257100
## 166 CAU436_xinlun5-9 SRR448743.sra 13135398 3006112
## 167 CAU439_lv45 SRR448744.sra 19351848 3100024
## 168 CAU446_fengke1 SRR448745.sra 17062436 3464142
## 169 CAU448_ernan24 SRR448788.sra 51297372 10693024
## 170 CAU451_78371A SRR448789.sra 38396086 7848628
## 171 CAU452_PHT10 SRR448790.sra 27223816 4529592
## 172 CAU453_PHH93 SRR448831.sra 16467204 3917056
## 173 CAU454_IBB14 SRR448832.sra 17286440 3527718
## 174 CAU458_LH149 SRR448879.sra 3322598 635170
## 175 CAU458_LH149 SRR448880.sra 25074014 4217724
## 176 CAU461_794 SRR448881.sra 7766012 1819486
## 177 CAU461_794 SRR448922.sra 30885128 5082484
## 178 CAU463_PHR32 SRR448923.sra 24347112 5516172
## 179 CAU465_PHG50 SRR448924.sra 2392706 548830
## 180 CAU465_PHG50 SRR448925.sra 27067494 4308112
## 181 CAU466_LH51 SRR448926.sra 24514754 5270674
## 182 CAU468_78010 SRR448927.sra 24957792 4135438
## 183 CAU470_LH39 SRR448928.sra 47346598 9516500
## 184 CAU471_PHG84 SRR448929.sra 19190692 4203142
## 185 CAU475_LH57 SRR448930.sra 1326496 265166
## 186 CAU475_LH57 SRR448931.sra 32442772 5516488
## 187 CAU476_LH38 SRR448935.sra 7427714 1500818
## 188 CAU476_LH38 SRR448937.sra 25366422 4150886
## 189 CAU488_807 SRR448938.sra 3152966 635358
## 190 CAU488_807 SRR448939.sra 44556800 7217604
## 191 CAU489_OH43 SRR448940.sra 34891234 6743830
## 192 CAU490_PHN11 SRR448941.sra 27845008 5720112
## 193 CAU491_PHJ70 SRR448942.sra 15408466 3099366
## 194 CAU492_DJ7 SRR448943.sra 14604910 2927476
## 195 CAU496_790 SRR448944.sra 16010958 3005810
## 196 CAU497_PHZ51 SRR448945.sra 11095788 2428978
## 197 CAU497_PHZ51 SRR448946.sra 37173380 5787494
## 198 CAU498_PHT60 SRR448947.sra 14672326 2831634
## 199 CAU501_PHG83 SRR448948.sra 24963546 4963730
## 200 CAU503_PHJ75 SRR448950.sra 24255614 4798192
## 201 CAU505_PB80 SRR448951.sra 22006086 3943546
## 202 CAU510_LH52 SRR448952.sra 2443682 396424
## 203 CAU510_LH52 SRR448953.sra 25201100 3784010
## 204 CAU513_PHW52 SRR448954.sra 10133528 1862242
## 205 CAU513_PHW52 SRR448955.sra 19248702 3764786
## 206 CAU514_LH93 SRR448956.sra 17937758 3602222
## 207 CAU515_PHM57 SRR448957.sra 18160324 3414812
## 208 CAU517_LH60 SRR448958.sra 11542092 1938228
## 209 CAU518_PHG71 SRR448959.sra 6444370 1219196
## 210 CAU518_PHG71 SRR448960.sra 20789222 3366642
## 211 CAU520_Q381 SRR448961.sra 5638950 1028648
## 212 CAU520_Q381 SRR448962.sra 34946194 5666410
## 213 CAU521_MBPM SRR448963.sra 3775604 670196
## 214 CAU521_MBPM SRR449014.sra 38906294 6342056
## 215 CAU522_PHW03 SRR449015.sra 4248878 768312
## 216 CAU522_PHW03 SRR449016.sra 42596872 6756184
## 217 CAU523_PHW43 SRR449084.sra 4712530 849778
## 218 CAU523_PHW43 SRR449085.sra 24957234 3896062
## 219 CAU525_LH190 SRR449086.sra 19428764 3612554
## 220 CAU526_B47 SRR449087.sra 16673356 3201398
## 221 CAU527_PHV78 SRR449088.sra 33896930 5777572
## 222 CAU528 SRR449089.sra 26776384 4773208
## 223 CAU530_PHK76 SRR449090.sra 15637598 2852882
## 224 CAU531_LH1 SRR449091.sra 28888098 4824016
## 225 CAU534_PHJ31 SRR449093.sra 6836046 1359164
## 226 CAU534_PHJ31 SRR449094.sra 27022430 4318054
## 227 CAU535_78002A SRR449095.sra 12359978 2189140
## 228 CAU536_792 SRR449096.sra 15571138 2693542
## 229 CAU537_PHJ40 SRR449097.sra 14305712 2692058
## 230 CAU538_LH54 SRR449098.sra 29822450 5859754
## 231 CAU539_FAPW SRR449099.sra 13855698 2729518
## 232 CAU541_LH205 SRR449100.sra 6686916 1183800
## 233 CAU541_LH205 SRR449101.sra 26913786 4035692
## 234 CAU542_LH127 SRR449102.sra 6499730 1108574
## 235 CAU542_LH127 SRR449103.sra 31835558 4951568
## 236 CAU545_LH194 SRR449104.sra 8942462 1536308
## 237 CAU545_LH194 SRR449105.sra 23516160 3599294
## 238 CAU546_LH202 SRR449106.sra 12784704 2277500
## 239 CAU549_RS710 SRR449107.sra 5374822 979868
## 240 CAU549_RS710 SRR449108.sra 37131270 5331778
## 241 CAU551_PHW51 SRR449109.sra 4193078 794202
## 242 CAU551_PHW51 SRR449111.sra 33812134 5213928
## 243 CAU566_PHP85 SRR449112.sra 2192628 418632
## 244 CAU566_PHP85 SRR449113.sra 40832968 6793558
## 245 CAU572_LH143 SRR449114.sra 45424196 8557614
## 246 CAU574_207 SRR449115.sra 32187896 6589784
## 247 CAU575_CR1HT SRR449116.sra 22334204 5117664
## 248 CAU576_6103 SRR449117.sra 31294368 6144240
## 249 CAU578_4676A SRR449118.sra 22271324 4337974
## 250 CAU580_PHR36 SRR449119.sra 15217972 3136904
## 251 CAU582_IB02 SRR449120.sra 20452374 4490050
## 252 CAU583_IBB15 SRR449121.sra 60859244 11608088
## 253 CAU584_787 SRR449122.sra 24028150 4966750
## 254 CAU586_11430 SRR449123.sra 31988400 5883362
## 255 CAU587_2369 SRR449124.sra 21612894 4690528
## 256 CAU588_2MA22 SRR449125.sra 18034864 3344524
## 257 CAU590_MBST SRR449126.sra 41546176 9744790
## 258 CAU591_PHN47 SRR449127.sra 27976220 5118902
## 259 CAU592_NS501 SRR449128.sra 20038518 3993050
## 260 CAU593_H8431 SRR449129.sra 19671692 3595126
## 261 CAU594_S8324 SRR449130.sra 22481614 4236580
## 262 CAU595_CR14 SRR449131.sra 20072752 3564632
## 263 CAU596_WIL901 SRR449132.sra 18071980 3262266
## 264 CAU597_WIL903 SRR449179.sra 20436838 3680832
## 265 CAU598_WIL500 SRR449180.sra 15841086 3076686
## 266 CAU599_E8501 SRR449181.sra 27252312 5938352
## 267 CAU601_L135 SRR449183.sra 16340354 3153860
## 268 CAU604_PHM10 SRR449184.sra 7805614 1430290
## 269 CAU604_PHM10 SRR449185.sra 36099212 5511284
## 270 CAU605_PHN82 SRR449186.sra 10203788 1869788
## 271 CAU605_PHN82 SRR449187.sra 43774412 6697950
## 272 CAU607_PHR63 SRR449188.sra 9401472 1823460
## 273 CAU607_PHR63 SRR449189.sra 45185352 7326224
## 274 CAU610_PHW20 SRR449190.sra 3268806 571084
## 275 CAU610_PHW20 SRR449191.sra 38497232 5942532
## 276 CAU611_W23 SRR449192.sra 15996812 2746582
## 277 CAU631_PHP55 SRR449193.sra 9467360 1699938
## 278 CAU631_PHP55 SRR449194.sra 38194436 5982648
## 279 CAU638_huobai SRR449195.sra 36615310 7423520
## 280 CAU69_qi410 SRR449196.sra 1358570 288160
## 281 CAU77_DH149 SRR449198.sra 28332774 4480240
## 282 CAU78_R08 SRR449199.sra 30245972 5501286
## 283 CAU84_B95 SRR449200.sra 32323478 6148002
## 284 CAU84_B95 SRR449201.sra 51188154 10171574
## 285 CAU97_guan17-1 SRR449202.sra 13398930 2532572
## 286 CAU98_wu125 SRR449203.sra 9511846 1934918
## 287 CAU98_wu125 SRR449204.sra 24757538 5163632
## 288 CAU31_wu126 SRR449205.sra 3687376 642240
## 289 CAU31_wu126 SRR449206.sra 30808352 4370084
## 290 CAU33_yi36 SRR449207.sra 19150348 3609798
## 291 CAU39_CM105 SRR449208.sra 35507966 7418806
## 292 CAU41_P39 SRR449209.sra 21152882 4130530
## 293 CAU42_shangyin110-1 SRR449210.sra 31637448 6536124
## 294 CAU46_zhong451 SRR449211.sra 23330134 3756148
## 295 CAU47_huotanghuang17 SRR449212.sra 8979448 1544050
## 296 CAU47_huotanghuang17 SRR449213.sra 39124970 6629386
## 297 CAU58_B12 SRR449214.sra 55246422 11333152
## 298 CAU609_PHV37 SRR449215.sra 39572220 6189458
## 299 CAU61_ji870 SRR449216.sra 12842658 2199706
## 300 CAU63_fu8521 SRR449217.sra 2017800 334268
## 301 CAU63_fu8521 SRR449218.sra 21445858 3186802
## 302 CAU68_jiao05 SRR449219.sra 39184422 6538198
## 303 CAU73_xiangai3 SRR449244.sra 67847256 12686410
## 304 CAU74_fusheA SRR449245.sra 49663004 9522120
## 305 CAU76_qiong51 SRR449246.sra 56386014 9991402
## 306 CAU547_LH191_1 SRR449248.sra 10986988 2012530
## 307 CAU547_LH191_2 SRR449249.sra 23370308 4370152
## 308 CAU548_LH192_1 SRR449264.sra 10404602 1918910
## 309 CAU548_LH192_2 SRR449267.sra 14114950 2674464
## 310 CAU577_IB014_1 SRR449268.sra 9433494 1933686
## 311 CAU577_IB014_2 SRR449269.sra 11484214 2381224
## 312 CAU581_NS701_1 SRR449271.sra 10225760 2162872
## 313 CAU581_NS701_2 SRR449273.sra 9668562 2047928
## 314 CAU589_87916W_1 SRR449274.sra 10897408 2233968
## 315 CAU589_87916W_2 SRR449276.sra 8567546 1780338
## 316 CAU606_PHP60_1 SRR449277.sra 10784408 1994682
## 317 CAU606_PHP60_2 SRR449278.sra 7527680 1448564
## 318 CAU38_A632 SRR449338.sra 54670562 10542594
## 319 CAU38_A632 SRR449339.sra 200090816 37829378
## 320 CAU01_zheng58 SRR449340.sra 209836566 36830506
## 321 CAU01_zheng58 SRR449342.sra 210299448 37038186
## 322 CAU01_zheng58 SRR449343.sra 209479760 36852232
## 323 CAU02_chang7-2 SRR449344.sra 219172950 36372728
## 324 CAU02_chang7-2 SRR449345.sra 219903720 36542418
## 325 CAU02_chang7-2 SRR449346.sra 202884762 37462684
## 326 CAU05_478 SRR449347.sra 205982796 38074152
## 327 CAU05_478 SRR449348.sra 71938362 12098038
## 328 CAU06_zong31 SRR449350.sra 66064604 11244012
## 329 CAU07_D340 SRR449351.sra 62306128 10849212
## 330 CAU08_H127 SRR449352.sra 209405228 35893810
## 331 CAU04_5003 SRR449353.sra 207150544 35513044
## 332 CAU04_5003 SRR449354.sra 204067978 34914546
## 333 CAU04_5003 SRR449355.sra 72580986 12707456
## 334 CAU27_ye8112_1 SRR449357.sra 72376612 12683146
## 335 CAU27_ye8112_2 SRR449358.sra 72449758 12695284
## 336 CAU27_ye8112_2 SRR449359.sra 56753674 10369628
## 337 CAU196_ji846 SRR449427.sra 58554706 9119834
## 338 Mo17 SRR449556.sra 76591152 11816000
## 339 Mo17 SRR449557.sra 84941176 13041504
## 340 Mo17 SRR449558.sra 70680044 12453996
## 341 CAU27_ye8112_1 SRR528558.sra 203355090 37623062
## 342 CAU05_478 SRR528559.sra 36928096 3697896
## 343 CAU01_Zheng58_BGI_1 SRR530830.sra 40903792 4174366
## 344 CAU01_Zheng58_BGI_1 SRR530831.sra 60988392 9313760
## 345 CAU01_Zheng58_BGI_2 SRR530833.sra 9272124 975774
## 346 CAU05_478_BGI_1 SRR530834.sra 20982640 2080560
## 347 CAU05_478_BGI_1 SRR530835.sra 75418054 10976936
## 348 CAU05_478_BGI_2 SRR530836.sra 90285180 12982446
## 349 CAU05_478_BGI_2 SRR530837.sra 55939904 5374858
## 350 CAU04_5003_BGI_1 SRR530838.sra 15813344 2125642
## 351 CAU04_5003_BGI_2 SRR530840.sra 18506722 2258522
## 352 CAU04_5003_BGI_2 SRR530841.sra 12588218 3247456
## 353 CAU223_H99 SRR671686.sra 12455832 2623574
## 354 CAU268_B8 SRR671687.sra 11033640 2560600
## 355 CAU272_M14 SRR671688.sra 9432854 2124502
## 356 CAU364_B7 SRR671689.sra 14817490 2766176
## 357 CAU427_H105W SRR671715.sra 18324180 4361122
## 358 CAU532_PHG35 SRR671716.sra 8281690 2321994
## 359 CAU308_W117 SRR801200.sra 6667542 1676960
## 360 CAU421_CI66 SRR801201.sra 6667542 1676960
N = (x$Line)
x$Accession = NULL
fbyN = factor(N, exclude = " ")
x$Line = NULL
abun = aggregate(x, by = list(fbyN), FUN = "mean", na.rm = T)
abun2 = Filter(function(abun) !all(is.na(abun)), abun)
A = (abun2$Group.1)
B = (abun2$Total_Reads)
C = (abun2$Reads_Mapped)
## Percent reads mapped per lane
D = (abun2$Reads_Mapped/abun2$Total_Reads) * 100
abun3 = data.frame(A, B, C, D)
Columns
$A = Lines $B = Total_Reads $C = Reads_Mapped $D = Percent Abundance
print(abun3)
## A B C D
## 1 CAU01_zheng58 209871925 36906975 17.59
## 2 CAU01_Zheng58_BGI_1 50946092 6744063 13.24
## 3 CAU01_Zheng58_BGI_2 9272124 975774 10.52
## 4 CAU02_chang7-2 213987144 36792610 17.19
## 5 CAU04_5003 161266503 27711682 17.18
## 6 CAU04_5003_BGI_1 15813344 2125642 13.44
## 7 CAU04_5003_BGI_2 15547470 2752989 17.71
## 8 CAU05_478 104949751 17956695 17.11
## 9 CAU05_478_BGI_1 48200347 6528748 13.55
## 10 CAU05_478_BGI_2 73112542 9178652 12.55
## 11 CAU06_zong31 68220693 11497837 16.85
## 12 CAU07_D340 64443910 11108865 17.24
## 13 CAU08_H127 135951743 23389145 17.20
## 14 CAU10_yu87-1 73922520 11709106 15.84
## 15 CAU100_shen5005 12789712 2223822 17.39
## 16 CAU103_807D 16378630 3234612 19.75
## 17 CAU105_1145 27788671 5633142 20.27
## 18 CAU107_D15 53884742 11162194 20.71
## 19 CAU11_longkang11 71303880 10754688 15.08
## 20 CAU112_S22 27992552 5631410 20.12
## 21 CAU114_Q1261 43688370 9250550 21.17
## 22 CAU115_ye52106 50694684 10155080 20.03
## 23 CAU116_1205A 54989120 11482296 20.88
## 24 CAU118_K12 66325306 15186432 22.90
## 25 CAU12_danhuang02 70550372 10938700 15.50
## 26 CAU120_xing230 37539234 7278254 19.39
## 27 CAU125_K22 29288693 5803616 19.82
## 28 CAU129_P007 24669700 5800526 23.51
## 29 CAU131_Yd6 39565846 8794128 22.23
## 30 CAU132_IA5125 35050790 7060990 20.15
## 31 CAU133_liao2202 11549652 2458770 21.29
## 32 CAU134_dai6 31403208 6243232 19.88
## 33 CAU137_W499 34527392 7301770 21.15
## 34 CAU14_shen137 47654598 7552766 15.85
## 35 CAU140_XOP2 44393734 9391928 21.16
## 36 CAU142_D20 38222516 8206698 21.47
## 37 CAU143_hai1134 43072954 8841202 20.53
## 38 CAU144_yu374 32366838 6705910 20.72
## 39 CAU146_dan9064 49559620 10763872 21.72
## 40 CAU147_niu2-1 13595750 3157190 23.22
## 41 CAU148_suwan1611 44226768 11195502 25.31
## 42 CAU149_R017 34152220 6526300 19.11
## 43 CAU15_zheng22 29831374 4275576 14.33
## 44 CAU151_shen977 20031072 4186144 20.90
## 45 CAU156_huangchangb 11536754 2907194 25.20
## 46 CAU16_lv28 57801942 8678496 15.01
## 47 CAU164_K10 19411754 3579474 18.44
## 48 CAU165_ye5237 24808102 4852162 19.56
## 49 CAU166_zheng32 52716414 9729032 18.46
## 50 CAU17_huangC 57657996 9121656 15.82
## 51 CAU173_P167 28778874 5424846 18.85
## 52 CAU174_R31 23687032 4552484 19.22
## 53 CAU178_changK 95390126 20486192 21.48
## 54 CAU18_P138 20635296 3177444 15.40
## 55 CAU180_M131-5 61963408 14425670 23.28
## 56 CAU19_zi330 20231930 2210504 10.93
## 57 CAU191_hai014 29611676 5474032 18.49
## 58 CAU192_ji444 32494330 6051942 18.62
## 59 CAU193_ben7884 26919086 5189638 19.28
## 60 CAU194_huangyesi3 54939872 9975014 18.16
## 61 CAU195_zaC546 26994450 4421520 16.38
## 62 CAU196_ji846 58554706 9119834 15.57
## 63 CAU197_4F1 54271394 10270554 18.92
## 64 CAU198_wenhuang31413 40677216 7323818 18.00
## 65 CAU199_ye515 28517790 5336274 18.71
## 66 CAU20_huangzaosi 191447520 25081664 13.10
## 67 CAU200_hu803 30975942 6052586 19.54
## 68 CAU201_tian77 25215182 4673270 18.53
## 69 CAU202_ye488 34138340 6385208 18.70
## 70 CAU203_chang72 35114958 6790090 19.34
## 71 CAU207_3H2 30523744 5385740 17.64
## 72 CAU208_cheng698-3 45368756 8679264 19.13
## 73 CAU21_tie7922 34680814 5360994 15.46
## 74 CAU210_su75 22744484 4360312 19.17
## 75 CAU211_Beck 24646984 4602166 18.67
## 76 CAU215_P136 21909330 4316120 19.70
## 77 CAU217_dan9046 111018246 21607698 19.46
## 78 CAU223_H99 12455832 2623574 21.06
## 79 CAU224_W64a 28359710 5473788 19.30
## 80 CAU225_A554 22630300 4665756 20.62
## 81 CAU229_xun92-8 25377004 4925178 19.41
## 82 CAU234_H21 8492012 1256700 14.80
## 83 CAU235_shuang741 8086024 1209596 14.96
## 84 CAU236_200B 15696383 2492282 15.88
## 85 CAU237_chong72 8352132 1179981 14.13
## 86 CAU238_Pa91 9226741 1374762 14.90
## 87 CAU239_yu537A 9185820 1446043 15.74
## 88 CAU24_9058 31348844 5085218 16.22
## 89 CAU242_dan3115 38621670 7267130 18.82
## 90 CAU244_zhonghuang64 37965758 6984874 18.40
## 91 CAU247_dong327 20027474 3752498 18.74
## 92 CAU248_698-3 32166979 6706404 20.85
## 93 CAU25_ji853 32946090 5387742 16.35
## 94 CAU251_N138 27997628 5652580 20.19
## 95 CAU254_DM07 22297332 4612229 20.69
## 96 CAU256_B100 15007344 3602100 24.00
## 97 CAU257_B98 60430820 13069752 21.63
## 98 CAU261_lian87 18835652 3785498 20.10
## 99 CAU264_L-1 23836414 5077832 21.30
## 100 CAU268_B8 11033640 2560600 23.21
## 101 CAU27_ye8112_1 137865851 25153104 18.24
## 102 CAU27_ye8112_2 64601716 11532456 17.85
## 103 CAU271_changD 40275098 8365370 20.77
## 104 CAU272_M14 9432854 2124502 22.52
## 105 CAU273_M101 30015712 6664942 22.20
## 106 CAU275_B394 24324930 5423104 22.29
## 107 CAU282_R25 20277017 4239643 20.91
## 108 CAU283_chengzi108 45409046 9737886 21.44
## 109 CAU289_ye107 24778212 4559804 18.40
## 110 CAU29_Maxa 23834972 3878808 16.27
## 111 CAU290_jiutai1 35807010 7149786 19.97
## 112 CAU294_hai9-21 24543810 5083818 20.71
## 113 CAU295_ji533 16686880 3254602 19.50
## 114 CAU297_ye832 11611344 2265496 19.51
## 115 CAU302_B76 11529413 1914358 16.60
## 116 CAU303_NC268 14901603 3037807 20.39
## 117 CAU306_Sg1533 10210041 1628493 15.95
## 118 CAU308_W117 6667542 1676960 25.15
## 119 CAU31_wu126 17247864 2506162 14.53
## 120 CAU310_7327 26394368 4938050 18.71
## 121 CAU316_bao3040 28479496 5103702 17.92
## 122 CAU320_Lx9801 8061178 1231170 15.27
## 123 CAU326_shen135 72810158 16662060 22.88
## 124 CAU33_yi36 19150348 3609798 18.85
## 125 CAU332_baihe43 18272456 3290242 18.01
## 126 CAU34_nan21-3 33473400 5738410 17.14
## 127 CAU345_jiu138-5 49445552 9782372 19.78
## 128 CAU347_ning55 29818296 5826008 19.54
## 129 CAU350_han21 28387428 5248956 18.49
## 130 CAU355_huotanghuang 34007834 6341528 18.65
## 131 CAU357_yu82 24395098 4807752 19.71
## 132 CAU359_CN165 20832640 3958900 19.00
## 133 CAU361_fu8701 20832656 3876936 18.61
## 134 CAU362_De811 15560462 3300838 21.21
## 135 CAU364_B7 14817490 2766176 18.67
## 136 CAU365_shan89 23009056 4444022 19.31
## 137 CAU366_A679 20209040 4313716 21.35
## 138 CAU367_Va26 18880484 3555156 18.83
## 139 CAU370_E28 15504016 3092554 19.95
## 140 CAU372_zhongyin15 13564720 2794724 20.60
## 141 CAU375_zong3 22205934 3568896 16.07
## 142 CAU38_A632 127380689 24185986 18.99
## 143 CAU382_FC-13 22939622 4386848 19.12
## 144 CAU384_ji63 10387473 1829211 17.61
## 145 CAU385_ji434 34144328 5711746 16.73
## 146 CAU386_ji4112 13421375 2329417 17.36
## 147 CAU389_qi205 14504146 2837000 19.56
## 148 CAU39_CM105 35507966 7418806 20.89
## 149 CAU40_B68 13707906 2800868 20.43
## 150 CAU400_P25 32540712 6885722 21.16
## 151 CAU401_R98 26806642 5992190 22.35
## 152 CAU402_qi319 13622275 2790597 20.49
## 153 CAU405_huo17 28925422 5379644 18.60
## 154 CAU409_huangyesi 37270516 8593738 23.06
## 155 CAU41_P39 21152882 4130530 19.53
## 156 CAU411_shen142 21836150 5083134 23.28
## 157 CAU413_siyi 19122334 4543392 23.76
## 158 CAU416_xun971 15537756 3497108 22.51
## 159 CAU42_shangyin110-1 31637448 6536124 20.66
## 160 CAU420_Mo24W 33310432 7167320 21.52
## 161 CAU421_CI66 6667542 1676960 25.15
## 162 CAU422_W182bn 26094066 5227134 20.03
## 163 CAU423_W153R 13367274 2777645 20.78
## 164 CAU425_HP301 12514436 2547363 20.36
## 165 CAU426_H84 17247522 3647308 21.15
## 166 CAU427_H105W 18324180 4361122 23.80
## 167 CAU429_tangsipingtou 38921910 8992336 23.10
## 168 CAU434_cheng18 49503480 10257100 20.72
## 169 CAU436_xinlun5-9 13135398 3006112 22.89
## 170 CAU439_lv45 19351848 3100024 16.02
## 171 CAU446_fengke1 17062436 3464142 20.30
## 172 CAU448_ernan24 51297372 10693024 20.85
## 173 CAU451_78371A 38396086 7848628 20.44
## 174 CAU452_PHT10 27223816 4529592 16.64
## 175 CAU453_PHH93 16467204 3917056 23.79
## 176 CAU454_IBB14 17286440 3527718 20.41
## 177 CAU458_LH149 14198306 2426447 17.09
## 178 CAU46_zhong451 23330134 3756148 16.10
## 179 CAU461_794 19325570 3450985 17.86
## 180 CAU463_PHR32 24347112 5516172 22.66
## 181 CAU465_PHG50 14730100 2428471 16.49
## 182 CAU466_LH51 24514754 5270674 21.50
## 183 CAU468_78010 24957792 4135438 16.57
## 184 CAU47_huotanghuang17 24052209 4086718 16.99
## 185 CAU470_LH39 47346598 9516500 20.10
## 186 CAU471_PHG84 19190692 4203142 21.90
## 187 CAU475_LH57 16884634 2890827 17.12
## 188 CAU476_LH38 16397068 2825852 17.23
## 189 CAU488_807 23854883 3926481 16.46
## 190 CAU489_OH43 34891234 6743830 19.33
## 191 CAU490_PHN11 27845008 5720112 20.54
## 192 CAU491_PHJ70 15408466 3099366 20.11
## 193 CAU492_DJ7 14604910 2927476 20.04
## 194 CAU496_790 16010958 3005810 18.77
## 195 CAU497_PHZ51 24134584 4108236 17.02
## 196 CAU498_PHT60 14672326 2831634 19.30
## 197 CAU501_PHG83 24963546 4963730 19.88
## 198 CAU503_PHJ75 24255614 4798192 19.78
## 199 CAU505_PB80 22006086 3943546 17.92
## 200 CAU510_LH52 13822391 2090217 15.12
## 201 CAU513_PHW52 14691115 2813514 19.15
## 202 CAU514_LH93 17937758 3602222 20.08
## 203 CAU515_PHM57 18160324 3414812 18.80
## 204 CAU517_LH60 11542092 1938228 16.79
## 205 CAU518_PHG71 13616796 2292919 16.84
## 206 CAU520_Q381 20292572 3347529 16.50
## 207 CAU521_MBPM 21340949 3506126 16.43
## 208 CAU522_PHW03 23422875 3762248 16.06
## 209 CAU523_PHW43 14834882 2372920 16.00
## 210 CAU525_LH190 19428764 3612554 18.59
## 211 CAU526_B47 16673356 3201398 19.20
## 212 CAU527_PHV78 33896930 5777572 17.04
## 213 CAU528 26776384 4773208 17.83
## 214 CAU530_PHK76 15637598 2852882 18.24
## 215 CAU531_LH1 28888098 4824016 16.70
## 216 CAU532_PHG35 8281690 2321994 28.04
## 217 CAU534_PHJ31 16929238 2838609 16.77
## 218 CAU535_78002A 12359978 2189140 17.71
## 219 CAU536_792 15571138 2693542 17.30
## 220 CAU537_PHJ40 14305712 2692058 18.82
## 221 CAU538_LH54 29822450 5859754 19.65
## 222 CAU539_FAPW 13855698 2729518 19.70
## 223 CAU541_LH205 16800351 2609746 15.53
## 224 CAU542_LH127 19167644 3030071 15.81
## 225 CAU545_LH194 16229311 2567801 15.82
## 226 CAU546_LH202 12784704 2277500 17.81
## 227 CAU547_LH191_1 10986988 2012530 18.32
## 228 CAU547_LH191_2 23370308 4370152 18.70
## 229 CAU548_LH192_1 10404602 1918910 18.44
## 230 CAU548_LH192_2 14114950 2674464 18.95
## 231 CAU549_RS710 21253046 3155823 14.85
## 232 CAU551_PHW51 19002606 3004065 15.81
## 233 CAU566_PHP85 21512798 3606095 16.76
## 234 CAU572_LH143 45424196 8557614 18.84
## 235 CAU574_207 32187896 6589784 20.47
## 236 CAU575_CR1HT 22334204 5117664 22.91
## 237 CAU576_6103 31294368 6144240 19.63
## 238 CAU577_IB014_1 9433494 1933686 20.50
## 239 CAU577_IB014_2 11484214 2381224 20.73
## 240 CAU578_4676A 22271324 4337974 19.48
## 241 CAU58_B12 55246422 11333152 20.51
## 242 CAU580_PHR36 15217972 3136904 20.61
## 243 CAU581_NS701_1 10225760 2162872 21.15
## 244 CAU581_NS701_2 9668562 2047928 21.18
## 245 CAU582_IB02 20452374 4490050 21.95
## 246 CAU583_IBB15 60859244 11608088 19.07
## 247 CAU584_787 24028150 4966750 20.67
## 248 CAU586_11430 31988400 5883362 18.39
## 249 CAU587_2369 21612894 4690528 21.70
## 250 CAU588_2MA22 18034864 3344524 18.54
## 251 CAU589_87916W_1 10897408 2233968 20.50
## 252 CAU589_87916W_2 8567546 1780338 20.78
## 253 CAU590_MBST 41546176 9744790 23.46
## 254 CAU591_PHN47 27976220 5118902 18.30
## 255 CAU592_NS501 20038518 3993050 19.93
## 256 CAU593_H8431 19671692 3595126 18.28
## 257 CAU594_S8324 22481614 4236580 18.84
## 258 CAU595_CR14 20072752 3564632 17.76
## 259 CAU596_WIL901 18071980 3262266 18.05
## 260 CAU597_WIL903 20436838 3680832 18.01
## 261 CAU598_WIL500 15841086 3076686 19.42
## 262 CAU599_E8501 27252312 5938352 21.79
## 263 CAU601_L135 16340354 3153860 19.30
## 264 CAU604_PHM10 21952413 3470787 15.81
## 265 CAU605_PHN82 26989100 4283869 15.87
## 266 CAU606_PHP60_1 10784408 1994682 18.50
## 267 CAU606_PHP60_2 7527680 1448564 19.24
## 268 CAU607_PHR63 27293412 4574842 16.76
## 269 CAU609_PHV37 39572220 6189458 15.64
## 270 CAU61_ji870 12842658 2199706 17.13
## 271 CAU610_PHW20 20883019 3256808 15.60
## 272 CAU611_W23 15996812 2746582 17.17
## 273 CAU63_fu8521 11731829 1760535 15.01
## 274 CAU631_PHP55 23830898 3841293 16.12
## 275 CAU638_huobai 36615310 7423520 20.27
## 276 CAU68_jiao05 39184422 6538198 16.69
## 277 CAU69_qi410 1358570 288160 21.21
## 278 CAU73_xiangai3 67847256 12686410 18.70
## 279 CAU74_fusheA 49663004 9522120 19.17
## 280 CAU76_qiong51 56386014 9991402 17.72
## 281 CAU77_DH149 28332774 4480240 15.81
## 282 CAU78_R08 30245972 5501286 18.19
## 283 CAU84_B95 41755816 8159788 19.54
## 284 CAU97_guan17-1 13398930 2532572 18.90
## 285 CAU98_wu125 17134692 3549275 20.71
## 286 Mo17 77404124 12437167 16.07
Statistical Summary
Stats for Percent Abundance
summary(D)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 10.5 17.1 19.0 18.9 20.6 28.0
Average Abundance Across Lines
mean(D)
## [1] 18.93
Plot showing Percent Reads Mapped per Lane.
hist(D, xlab = "Percent Reads Mapped", ylab = "Jiao Lines", xlim = c(5, 35),
ylim = c(0, 100), col = rgb(0.6, 0.7, 0.8, 0.9), main = "cDNA Abundance")