soap2结果分析

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？