doc/summary.md

In zhezhangsh/PAClindrome: Palindrome subsequences in PacBio long reads

Summary of consensus sequences is saved in the $output/consensus-summary.txt as a table, with columns give the following stats about each consensus:

• nBase: length of the consensus
• nPalin: total number of palindrome repeats used to draw the consensus
• nRemoved: number of palindromes not used for the consensus due to quality concerns
• mPalin: average number of palindromes used at each position within the consensus
• mPercent: average percentage of palindromes agree with the consensus at each position (100 if all palindromes have the same base at a position)
• mPhred: average log10-P value of proportion test on the percentage of palindromes agree with the consensus, at each position

Table 1 Summary of consensus sequences from test run.

| subread name | nBase | nPalin | nRemoved | mPalin | mPercent | mPhred | |------------------------------|-------|--------|---------|---------|----------|------| | m54215_191216_174243/4260227 | 1162 | 6 | 0 | 4.25 | 92.92 | 2.89 | | m54215_191216_174243/4325960 | 2635 | 8 | 0 | 7.22 | 93.01 | 5.17 | | m54215_191216_174243/4522859 | 887 | 26 | 12 | 13.64 | 90.98 | 9.5 | | m54215_200221_110350/4784809 | 2643 | 12 | 0 | 11.16 | 94 | 8.3 | | m54215_200221_110350/4980913 | 2508 | 3 | 1 | 2 | 97.43 | 1.22 | | m54215_200221_110350/4981702 | 718 | 17 | 3 | 13.51 | 92.79 | 9.84 |

Consensus sequencing meeting all of the following criteria are likely to have accuracy around 99.%. We recommend to use these sequences for de novo assembly, linkage analysis, low depth variant calling, and similar challenging tasks.

• mPalin: 6 or higher
• mPercent: 90 or higher
• mPhred: 3 or higher

zhezhangsh/PAClindrome documentation built on March 21, 2022, 1:07 a.m.