soap2结果分析

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soap的结果分析：

1) id of read

2) full sequence of read. the read will be converted to the complementary if mapped on the reverse chain of the reference;

3) quality of the sequence corresponding to sequence.

4) number of hits. #全部比对上的次数

5) a/b, flag only meaningful for pair-end alignment.

6) length of read.

7) alignment on the direct(+) or reverse(-) chain of the reference.

8) location of first bp on the reference, counted from 1.

9) types of hits.

0: exact match.

n: the number of mismatch

10) Reference allele->Offset--Query allele--Quality

11) n—M, Offset--Reference allele--Quality

example:

SRR068443.6657 CTACAAAGGACATGAACTCATGATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTG de`ddcecfbcdbffdcbcfee``fffe`ffff^fadaffdfafffeefffffcffeffffffceffee`ffefcfefffdefffffffffcffeffffff 800 a 101 - chr1 74158 1 C->21G37 101M 21C79

SRR068443.6657 GTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGC ffffffeecf^dddc^eeeefffcfffdf^d`dddeeeecceffcffffff^ffefffdfffdffafcfbdcbc^aY^c_Wcaaabbbb^eceabb\d_^a 800 b 101 + chr1 74014 1 C->52A38 101M 52C48

74001 CCACCCCACAACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATG 74050

74051 TGATCTCATTGTTCACTTCCCACCTATGAGTGAGAATATGCGGTGTTTGG 74100

74101 TTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAGTTTCATC 74150

74151 CATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTA 74200

74201 TTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTG 74250

74251 GACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATA 74300

74301 AACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGG 74350

74351 GTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCGA 74400

74401 GATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTA 74450

74451 CAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCA 74500

怎么判断插入序列的长度是多少？