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Results: 7

1.
Figure 5

Figure 5. From: Identification of genomic indels and structural variations using split reads.

The flowchart of the split-read analysis pipeline.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
2.
Figure 6

Figure 6. From: Identification of genomic indels and structural variations using split reads.

The conceptual diagrams of the split-read analysis. SVs can be detected by sequence reads spanning their break points. The split-read analysis can directly identify deletions, small insertions, and the boundaries of large insertions. After the identification of SVs, duplications and translocations can be isolated out based on matching of insertions and deletions. Breakages in blue genomic lines denote different chromosomes.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
3.
Figure 7

Figure 7. From: Identification of genomic indels and structural variations using split reads.

The curves of the threshold functions. Each SV call is scored by the number of supportive reads and the maximum centeredness in those reads. The thresholds on these two quantities are determined by two threshold functions, plotted as the read and the blue curves, respectively. The gray dashed curve is the threshold function for the number of supportive reads before rounding. The parameter values used for the shown functional curves are λ = 1, tn = 8, and tc = 0.7.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
4.
Figure 3

Figure 3. From: Identification of genomic indels and structural variations using split reads.

Effect of sequencing on SV identification. The lengths of the colored, the white, and the gray portions of each bar signify the percentages of the true positives, the false negatives, and the false positives, respectively. The bars in different shades of green and red are used for the true positive calls of deletion and insertion of different length. (A-B) Different read length. SV are calls for sets of simulated reads of different lengths with the same coverage (5×). (C-D) Different coverage. SV are calls for sets of simulated reads of the same lengths (~400-bp) with different coverage.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
5.
Figure 4

Figure 4. From: Identification of genomic indels and structural variations using split reads.

Discoverable simulated SVs. Not all SVs are identifiable, as some of them are not covered by any or enough sequence reads. The lengths of the gray and the colored portions of each bar signify the log-number of indels covered by only one and more than one read, respectively. The bars in different shades of green and red are used for the true positive calls of deletion and insertion of different length. A missing bar indicates a zero count. The counts of simulated deletions (A) and insertions (B) that are covered by at least two reads and by only one read are plotted as colored and gray bars.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
6.
Figure 2

Figure 2. From: Identification of genomic indels and structural variations using split reads.

Effect of different thresholds on SV identification. Different sets of indels are called at combinations of different values for thresholds tr, tn, and tc. Each bar shows the percentages of the true positives, the false negatives, and the false positives of each call set, which are represented by the colored, the white, and the gray portions, respectively. The bars in different shades of green and red are used for the true positive calls of deletion and insertion of different length. (A-B) The alignment score ratio threshold, tr. SV are calls for a set of simulated reads using different tr while tn = 5 and tc = 0.1 are kept unchanged. (C-D) The number of supportive read threshold, tn. SV are calls for the same set of simulated reads using different tn while tr = 1 and tc = 0.1 are kept unchanged. (E-F) The maximum centeredness threshold, tc. SV are calls for the same set of simulated reads using different tc while tn = 5 and tr = 1 are kept unchanged.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.
7.
Figure 1

Figure 1. From: Identification of genomic indels and structural variations using split reads.

The size spectrum of SVs identifiable to different methods. No method can identify SVs of all different sizes. The black bars indicate the size ranges of discoverable SVs by different methods, which include the dbSNP database, the high-resolution array CGH (hr-aCGH), the read-pair (RP) method with fosmid, 454, and Solexa sequencing, and the split-read analysis. The range of detectable indels by RP depends on three values: the mean and the standard deviation between the distances of mapped read pairs and the multiple coefficient of s.d. for significance. These triple values are (40 kb, 2.8 kb, 3), (1 kb, 0.8 kb, 3), (250 bp, 25 bp, 6) for fosmid, 454, and Solexa sequencing, respectively.

Zhengdong D Zhang, et al. BMC Genomics. 2011;12:375-375.

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