1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19

String encoding mismatched and deleted reference bases, used in conjunction with the CIGAR and SEQ fields to reconstruct the bases of the reference sequence interval to which the alignment has been mapped. This can enable variant calling without requiring access to the entire original reference.
编码错配或del的字符串，与CIGAR和SEQ一起使用，重建read的比对情况。可以在不需要整个参考序列的情况下，用于突变检测。

The MD string consists of the following items, concatenated without additional delimiter characters:
MD字符串由以下不含分隔符的条目组成。

• [0-9]+, indicating a run of reference bases that are identical to the corresponding SEQ bases;表示与相应SEQ碱基相同的一系列参考碱基；这里[0-9]+是正则表示。
• [A-Z], identifying a single reference base that differs from the SEQ base aligned at that position;在这个位置SEQ碱基与参考碱基不一致
• \^[A-Z]+, identifying a run of reference bases that have been deleted in the alignment.以^开头，表明有个del，注意del前有^。

总结：数字表示匹配，碱基表示错配，^碱基表示del。

As shown in the complete regular expression above, numbers alternate with the other items. Thus if two mismatches or deletions are adjacent without a run of identical bases between them, a ‘0’ (indicating a 0-length run) must be used to separate them in the MD string. 数字和字符交替出现，如果两个连续错配，中间需要用0来隔开。

Clipping, padding, reference skips, and insertions (‘H’, ‘S’, ‘P’, ‘N’, and ‘I’ CIGAR operations) are not represented in the MD string. When reconstructing the reference sequence, inserted and soft-clipped SEQ bases are omitted as determined by tracking ‘I’ and ‘S’ operations in the CIGAR string. (If the CIGAR string contains ‘N’ operations, then the corresponding skipped parts of the reference sequence cannot be reconstructed.)
Clipping, padding, reference skips, and insertions (‘H’, ‘S’, ‘P’, ‘N’, and ‘I’ CIGAR operations)不体现在MD字符串中，所以要与CIGAR结合。

For example, a string ‘10A5^AC6’ means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches.
10A5^AC6表示10个匹配（10），一个与A不匹配（A），2bp的del（^AC），6碱基的匹配。

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12

graph TB
    A[子宫内膜及非典型子宫内膜增生AEH及子宫内膜样子宫内膜癌ECC] --> B[细胞分群]
    B --> C[上皮细胞比例在AEH中增加,在EEC中进一步扩大,CNV变化大]
    B --> D[间质成纤维细胞比例下降]
    C --> F[RNA velocity分析,细胞相似性分析,MET marer基因分析等表明ECC不来源CAF]
    D --> F
    F --> G[EEC的上皮聚类,发现AEH特有非纤毛上皮亚群,并在ECC中存在,推测来源于正常的非纤毛上皮]    
    G --> H[EEC上皮细胞独有亚群为致癌亚群,RNA velocity分析非纤毛上皮腺细胞有可能是致癌亚群中存在的来源]
    H --> I[致癌亚群特征基因,发现LCN2和SAA1/2可能是子宫内膜早期肿瘤发生的一个特征]
    I --> J[类器官实验证明在正常子宫内膜和EEC中成纤维细胞是不可缺少的]
    J --> K[类器官实验证明在正常子宫内膜和EEC中成纤维细胞是不可缺少的]
    K --> L[巨噬细胞和淋巴细胞亚群分析表明免疫环境的失调可导致子宫内膜肿瘤的发生]