
精英版,覆盖率低的,其实是N的问题,和Y的重复片段问题。微基因覆盖率比Novaseq还要高,99.9%左右
统计的length_of_chromosome的长度是全部的碱基的长度,其中包含N,微基因统计的染色体长度是去掉N的,所以统计出来的覆盖率偏低(如21,22号染色体); Y染色体之所以更低是因为Y染色体中含有很多重复的序列,做比对分析的时候是把这些mask掉了(如果把这些也算进来会造成multimap的比例较高,不利于后面的分析),所以用来计算覆盖率的Y染色体的长度比实际的短很多。
纠正后。算出来都是99.9%了,而 illumina+抽血+Novaseq纠正后,算出来才 99.45%,额,微基因获胜。赞一个
{"1": {
"Breadth of Coverage": 0.903414844450879,
"Sum of Depths": 7746323812,
"Length": 249250621,
"Depth of Coverage": 31.07845340934978,
"Bases Mapped": 225176711
},
"2": {
"Breadth of Coverage": 0.9789934203489908,
"Sum of Depths": 8267303474,
"Length": 243199373,
"Depth of Coverage": 33.99393416199309,
"Bases Mapped": 238090586
},
"3": {
"Breadth of Coverage": 0.9832316874406601,
"Sum of Depths": 6567161240,
"Length": 198022430,
"Depth of Coverage": 33.16372412963521,
"Bases Mapped": 194701928
},
"4": {
"Breadth of Coverage": 0.9808907178199875,
"Sum of Depths": 6491206288,
"Length": 191154276,
"Depth of Coverage": 33.95794446157197,
"Bases Mapped": 187501455
},
"5": {
"Breadth of Coverage": 0.9816450585760428,
"Sum of Depths": 6022730733,
"Length": 180915260,
"Depth of Coverage": 33.29034119620423,
"Bases Mapped": 177594571
},
"6": {
"Breadth of Coverage": 0.9776568710924796,
"Sum of Depths": 5727330304,
"Length": 171115067,
"Depth of Coverage": 33.47063706552504,
"Bases Mapped": 167291821
},
"7": {
"Breadth of Coverage": 0.9753444265143788,
"Sum of Depths": 5295079454,
"Length": 159138663,
"Depth of Coverage": 33.273368986391446,
"Bases Mapped": 155215008
},
"8": {
"Breadth of Coverage": 0.9755289315566908,
"Sum of Depths": 4967270995,
"Length": 146364022,
"Depth of Coverage": 33.937786944663216,
"Bases Mapped": 142782338
},
"9": {
"Breadth of Coverage": 0.8498615404366175,
"Sum of Depths": 4036811065,
"Length": 141213431,
"Depth of Coverage": 28.586594323311925,
"Bases Mapped": 120011864
},
"10": {
"Breadth of Coverage": 0.9682194264176404,
"Sum of Depths": 4718124687,
"Length": 135534747,
"Depth of Coverage": 34.81118157102547,
"Bases Mapped": 131227375
},
"11": {
"Breadth of Coverage": 0.9709906298152305,
"Sum of Depths": 4465156822,
"Length": 135006516,
"Depth of Coverage": 33.07363936419188,
"Bases Mapped": 131090062
},
"12": {
"Breadth of Coverage": 0.9742425088565239,
"Sum of Depths": 4367468572,
"Length": 133851895,
"Depth of Coverage": 32.62911273687982,
"Bases Mapped": 130404206
},
"13": {
"Breadth of Coverage": 0.8296501538362314,
"Sum of Depths": 3222336816,
"Length": 115169878,
"Depth of Coverage": 27.978989575729166,
"Bases Mapped": 95550707
},
"14": {
"Breadth of Coverage": 0.8219577093669894,
"Sum of Depths": 2959153837,
"Length": 107349540,
"Depth of Coverage": 27.565594011860693,
"Bases Mapped": 88236782
},
"15": {
"Breadth of Coverage": 0.7964016132737182,
"Sum of Depths": 2749977602,
"Length": 102531392,
"Depth of Coverage": 26.820835534935487,
"Bases Mapped": 81656166
},
"16": {
"Breadth of Coverage": 0.8725298712287997,
"Sum of Depths": 2950990223,
"Length": 90354753,
"Depth of Coverage": 32.66004415949209,
"Bases Mapped": 78837221
},
"17": {
"Breadth of Coverage": 0.9573888164092439,
"Sum of Depths": 2657346142,
"Length": 81195210,
"Depth of Coverage": 32.72786833114909,
"Bases Mapped": 77735386
},
"18": {
"Breadth of Coverage": 0.9558745205773647,
"Sum of Depths": 2620507987,
"Length": 78077248,
"Depth of Coverage": 33.5630168086867,
"Bases Mapped": 74632052
},
"19": {
"Breadth of Coverage": 0.9429550479500045,
"Sum of Depths": 1838574649,
"Length": 59128983,
"Depth of Coverage": 31.094305291873532,
"Bases Mapped": 55755973
},
"20": {
"Breadth of Coverage": 0.9438193607922633,
"Sum of Depths": 2003332378,
"Length": 63025520,
"Depth of Coverage": 31.78605076165972,
"Bases Mapped": 59484706
},
"21": {
"Breadth of Coverage": 0.7288015068389407,
"Sum of Depths": 1296045756,
"Length": 48129895,
"Depth of Coverage": 26.928081933276605,
"Bases Mapped": 35077140
},
"22": {
"Breadth of Coverage": 0.6781870058115296,
"Sum of Depths": 1144507925,
"Length": 51304566,
"Depth of Coverage": 22.308110451611658,
"Bases Mapped": 34794090
},
"nuclear": {
"Depth of Coverage": 30.84477713274086,
"Length": 3095677412,
"Sum of Depths": 95485479848,
"Breadth of Coverage": 0.9228152128920855,
"Bases Mapped": 2856738210
},
"genome": {
"mt_ratio": 112.13839947691613,
"Bases Mapped": 2856754779,
"Breadth of Coverage": 0.9228156260061546,
"Sum of Depths": 95542790096,
"Length": 3095693981,
"Depth of Coverage": 30.86312493495784
},
"Y": {
"Breadth of Coverage": 0.3859570435772714,
"Sum of Depths": 705432982,
"Length": 59373566,
"Depth of Coverage": 11.881263490220547,
"Bases Mapped": 22915646
},
"X": {
"Breadth of Coverage": 0.972331239096452,
"Sum of Depths": 2665306105,
"Length": 155270560,
"Depth of Coverage": 17.16555994259311,
"Bases Mapped": 150974416
},
"MT": {
"Breadth of Coverage": 1,
"Sum of Depths": 57310248,
"Length": 16569,
"Depth of Coverage": 3458.883939887742,
"Bases Mapped": 16569
}
}
纠正后。算出来都是99.9%了,而 illumina+抽血+Novaseq纠正后,算出来才 99.45%,额,微基因获胜。赞一个
{"1": {
"Breadth of Coverage": 0.903414844450879,
"Sum of Depths": 7746323812,
"Length": 249250621,
"Depth of Coverage": 31.07845340934978,
"Bases Mapped": 225176711
},
"2": {
"Breadth of Coverage": 0.9789934203489908,
"Sum of Depths": 8267303474,
"Length": 243199373,
"Depth of Coverage": 33.99393416199309,
"Bases Mapped": 238090586
},
"3": {
"Breadth of Coverage": 0.9832316874406601,
"Sum of Depths": 6567161240,
"Length": 198022430,
"Depth of Coverage": 33.16372412963521,
"Bases Mapped": 194701928
},
"4": {
"Breadth of Coverage": 0.9808907178199875,
"Sum of Depths": 6491206288,
"Length": 191154276,
"Depth of Coverage": 33.95794446157197,
"Bases Mapped": 187501455
},
"5": {
"Breadth of Coverage": 0.9816450585760428,
"Sum of Depths": 6022730733,
"Length": 180915260,
"Depth of Coverage": 33.29034119620423,
"Bases Mapped": 177594571
},
"6": {
"Breadth of Coverage": 0.9776568710924796,
"Sum of Depths": 5727330304,
"Length": 171115067,
"Depth of Coverage": 33.47063706552504,
"Bases Mapped": 167291821
},
"7": {
"Breadth of Coverage": 0.9753444265143788,
"Sum of Depths": 5295079454,
"Length": 159138663,
"Depth of Coverage": 33.273368986391446,
"Bases Mapped": 155215008
},
"8": {
"Breadth of Coverage": 0.9755289315566908,
"Sum of Depths": 4967270995,
"Length": 146364022,
"Depth of Coverage": 33.937786944663216,
"Bases Mapped": 142782338
},
"9": {
"Breadth of Coverage": 0.8498615404366175,
"Sum of Depths": 4036811065,
"Length": 141213431,
"Depth of Coverage": 28.586594323311925,
"Bases Mapped": 120011864
},
"10": {
"Breadth of Coverage": 0.9682194264176404,
"Sum of Depths": 4718124687,
"Length": 135534747,
"Depth of Coverage": 34.81118157102547,
"Bases Mapped": 131227375
},
"11": {
"Breadth of Coverage": 0.9709906298152305,
"Sum of Depths": 4465156822,
"Length": 135006516,
"Depth of Coverage": 33.07363936419188,
"Bases Mapped": 131090062
},
"12": {
"Breadth of Coverage": 0.9742425088565239,
"Sum of Depths": 4367468572,
"Length": 133851895,
"Depth of Coverage": 32.62911273687982,
"Bases Mapped": 130404206
},
"13": {
"Breadth of Coverage": 0.8296501538362314,
"Sum of Depths": 3222336816,
"Length": 115169878,
"Depth of Coverage": 27.978989575729166,
"Bases Mapped": 95550707
},
"14": {
"Breadth of Coverage": 0.8219577093669894,
"Sum of Depths": 2959153837,
"Length": 107349540,
"Depth of Coverage": 27.565594011860693,
"Bases Mapped": 88236782
},
"15": {
"Breadth of Coverage": 0.7964016132737182,
"Sum of Depths": 2749977602,
"Length": 102531392,
"Depth of Coverage": 26.820835534935487,
"Bases Mapped": 81656166
},
"16": {
"Breadth of Coverage": 0.8725298712287997,
"Sum of Depths": 2950990223,
"Length": 90354753,
"Depth of Coverage": 32.66004415949209,
"Bases Mapped": 78837221
},
"17": {
"Breadth of Coverage": 0.9573888164092439,
"Sum of Depths": 2657346142,
"Length": 81195210,
"Depth of Coverage": 32.72786833114909,
"Bases Mapped": 77735386
},
"18": {
"Breadth of Coverage": 0.9558745205773647,
"Sum of Depths": 2620507987,
"Length": 78077248,
"Depth of Coverage": 33.5630168086867,
"Bases Mapped": 74632052
},
"19": {
"Breadth of Coverage": 0.9429550479500045,
"Sum of Depths": 1838574649,
"Length": 59128983,
"Depth of Coverage": 31.094305291873532,
"Bases Mapped": 55755973
},
"20": {
"Breadth of Coverage": 0.9438193607922633,
"Sum of Depths": 2003332378,
"Length": 63025520,
"Depth of Coverage": 31.78605076165972,
"Bases Mapped": 59484706
},
"21": {
"Breadth of Coverage": 0.7288015068389407,
"Sum of Depths": 1296045756,
"Length": 48129895,
"Depth of Coverage": 26.928081933276605,
"Bases Mapped": 35077140
},
"22": {
"Breadth of Coverage": 0.6781870058115296,
"Sum of Depths": 1144507925,
"Length": 51304566,
"Depth of Coverage": 22.308110451611658,
"Bases Mapped": 34794090
},
"nuclear": {
"Depth of Coverage": 30.84477713274086,
"Length": 3095677412,
"Sum of Depths": 95485479848,
"Breadth of Coverage": 0.9228152128920855,
"Bases Mapped": 2856738210
},
"genome": {
"mt_ratio": 112.13839947691613,
"Bases Mapped": 2856754779,
"Breadth of Coverage": 0.9228156260061546,
"Sum of Depths": 95542790096,
"Length": 3095693981,
"Depth of Coverage": 30.86312493495784
},
"Y": {
"Breadth of Coverage": 0.3859570435772714,
"Sum of Depths": 705432982,
"Length": 59373566,
"Depth of Coverage": 11.881263490220547,
"Bases Mapped": 22915646
},
"X": {
"Breadth of Coverage": 0.972331239096452,
"Sum of Depths": 2665306105,
"Length": 155270560,
"Depth of Coverage": 17.16555994259311,
"Bases Mapped": 150974416
},
"MT": {
"Breadth of Coverage": 1,
"Sum of Depths": 57310248,
"Length": 16569,
"Depth of Coverage": 3458.883939887742,
"Bases Mapped": 16569
}
}
2 个回复
赞同来自:
赞同来自:
要回复问题请先登录或注册