V300022071A

 a. Clean fastq is built by removing low-quality read from raw fastq. One pair of read is defined as low-quality when it:(1) contains adapter sequences, (2) N ratio > 1%, (3) the ratio of the base (base quality is lower than 10) > 10%.

 b. Q20 and Q30 means the ratio of base whose quality > 20 or 30 of the clean fastq.

 c. Total depth is calculated by the raw fastq.

Base distribution (x-axis is the sequencing cycle, y-axis is the proportion of five bases at a certain cycle).

Quality distribution (x-axis is the cycle along reads, y-axis is the heatmap of quality at given cycle).

 a. The barcodes of stLFR data are related to the Long-fragment read. We should do and filter and split the barcodes before we do next analysis. After this step, each read will get a barcode ID. The table above shows the barcode split statistics results.

Long-fragment vs. barcode in stLFR data (x-axis is average long-fragment DNA molecular number captured by barcode beads, y-axis is the density of barcode number).

Length distribution of long-fragment in stLFR data (x-axis is the length, y-axis is the count of long-fragment with given length).

Coverage of long-fragment of stLFR data (x-axis is the coverage of long-fragment, y-axis is the density of long-fragment at a certain coverage).

 a. The statistics results shown here are calculated based on clean data after low-quality filter and barcode-split filter.

 b. The mapping rate and paired mapping rate are the proportion of read which is mapped or paired-mapped to reference genome.

 c. The mismatch means the unmapped bases between read and reference genome.

 d. The duplication means duplicated reads introduced by PCR or other processes.

 e. The average sequencing depth is calculated by mapped reads without duplicated reads.

 f. The coverage is calculated as proportion of reference genome covered by more than 1, 4, 10 or 20 folds reads.

 g. The mean insert size is the mean insert size of paired mapped reads.

Insert size distribution (x-axis is insert size, y-axis is the count of paired reads at a certain insert size).

Cumulatived sequencing depth distribution (x-axis is the depth, y-axis is the proportion of reference genome that achieves at or above certain depth).

Sequencing depth distribution (x-axis is the depth, y-axis is the proportion of reference genome at a certain depth).

GC-bias distribution (x-aixs shows GC content, y-axis plots the NORMALIZED_COVERAGE, the distribution of WINDOWs corresponding to GC percentages, and base qualities corresponding to each GC content bin).

 a. SNP: Insertion& Deletion.

 b. Ti/TV：the ratio of transition (Ti) to transversion (Tv) SNPs.

 c. INDEL: Insertion & Deletion.

 d. CNV：copy number variant.

 e. SV: Structure Variant.

 f. DEL: deletion.

 g. DUP: duplication.

 h. INV: inversion.

 i. TRA: translocation.

 a. PPV: positive predictive value, precision, TP/(TP+FP).

 b. Sensitivity: true positive rate, TP/(TP+FN).

 c. F-measure: the harmonic mean of precision and sensitivity, 2*TP/(2*TP+FP+FN).

CIRCOS of variant from whole genome (From the outside to the inside are: (i) chromosomes, (ii) SNP densitity, (iii) INDEL densitity, (iv) CNV deletions, (v) CNV duplications and (vi) structure variants).

 a. switch rate: the fraction of switch errors.

 b. mismatch rate: the fraction of mismatch errors.

 c. flat rate: the fraction of flat errors.

 d. missing rate: the fraction missing errors.

 e. phased count: counts of total SNVs phased in the test haplotype.

 f. AN50: the phasing block AN50 length of haplotype completeness.

 g. N50: the phasing block N50 length of haplotype completeness.

 h. max block snp frac: the fraction of SNVs in the largest (most variants phased) block.

 i. phasing rate: the fraction of SNVs in all blocks.

The haplotype phasing plot (Each line shows one chrmosome. White shows no phasing block, where grey and dark-bule show phasing blocks).