Read summary
Read quality and length distributions, and the percentage yield for each read length, for reads above 100 bases and Q score 9. Use the dropdown menu to view the plots for the individual samples.
Filtering outcomes
Reads must pass several filtering checks
before being analysed. Reads which fail one check are excluded
from further checks. A failing read is tagged with a valid SAM tag
in the output BAM, in the format
qc:Z:<Status>
. Passing reads are tagged with the status:
Good
. Note that the median read length here is for the whole read, and not the telomeric repeats. The identity used here is gap-compressed identity, where a value of 1 represents a perfect alignment.
Status | Total reads | Median read length | Median quality | Median identity |
---|---|---|---|---|
TooFewRepeats | 9 | 4,864 | 21.73 | 0.99 |
StartNotRepeats | 71 | 6,760 | 15.16 | 0.98 |
TooCloseEnd | 4 | 2,236 | 20.73 | 1.0 |
LowSubTeloQual | 17 | 5,279 | 10.71 | 0.91 |
TelomereOnly | 4 | 1,907 | 18.93 | 0.99 |
TooErrorful | 96 | 8,368 | 14.93 | 0.97 |
BadAlign | 16 | 6,938 | 12.19 | 0.95 |
Good | 779 | 8,571 | 20.53 | 0.99 |
- TooShort - The read was too short (less than 160 bases).
- TooFewRepeats - There were fewer than 20 telomeric repeat motifs across the entire read.
- TooCloseStart - The telomeric boundary is too close (within 60 bases) to the read start.
- TooCloseEnd - The telomeric boundary is too close (within 60 bases) to the read end.
- StartNotRepeats - The first 30% of the read is < 80% repeats.
- LowSubTeloQual - The mean basecall Q score of the region after the boundary is below 9.
- TelomereOnly - Sequence after boundary is rich in CCC kmers, and is likely extra telomere after a misidentified boundary.
- TooErrorful - A large number of known basecalling error motifs have been observed in the subtelomere.
- BadAlign - A low gap-compressed identity to the reference or low mapQ score. Only applicable to aligned reads.
- Good - Passes all filtering, and is included in final analyses of telomere lengths.
Alignment-free telomere measurements
Bulk estimate(s) of telomere lengths from reads passing all QC steps. In the event no reads passed for a sample, all values will be 0. Note: The min and max values are within the median +/- 1.5X interquartile range. The coefficient of variation (CV) is a statistical measure that expresses the dispersion of data points around the mean, calculated as the ratio of the standard deviation to the mean. A lower value indicates less variation in measured telomere lengths.
Sample | Read count | Min length | Q1 | Median length | Q3 | Max length | CV |
---|---|---|---|---|---|---|---|
HG002_small_test | 758 | 104 | 1,943 | 3,026 | 4,507 | 8,334 | 0.58 |
Single molecule telomere lengths
Kernel density plots of all QC passing reads for each sample. These plots show the distribution of lengths of all telomeric reads in the chosen sample.
Aligned telomere lengths per contig
Telomere length metrics grouped by contig. Only primary alignments from reads which passed the QC filtering stages above are considered. Supplementary and secondary alignments for reads are not included. Note: The min and max values are within the median +/- 1.5X interquartile range. The coefficient of variation (CV) is a statistical measure that expresses the dispersion of data points around the mean, calculated as the ratio of the standard deviation to the mean. A lower value indicates less variation in measured telomere lengths.
Contig name | Read count | Min length | Q1 | Median length | Q3 | Max length | CV |
---|---|---|---|---|---|---|---|
chr1_MATERNAL_P | 9 | 3,268 | 3,462 | 3,873 | 4,024 | 4,455 | 0.2 |
chr1_MATERNAL_Q | 7 | 3,523 | 4,344 | 7,516 | 7,715 | 7,778 | 0.51 |
chr1_PATERNAL_P | 9 | 6,198 | 7,133 | 8,114 | 9,770 | 10,748 | 0.36 |
chr1_PATERNAL_Q | 10 | 1,246 | 3,446 | 4,694 | 6,408 | 7,629 | 0.42 |
chr2_MATERNAL_P | 9 | 3,338 | 3,871 | 4,084 | 6,427 | 7,268 | 0.31 |
chr2_MATERNAL_Q | 9 | 2,034 | 2,250 | 2,837 | 4,237 | 5,037 | 0.36 |
chr2_PATERNAL_P | 6 | 1,463 | 1,658 | 1,891 | 2,399 | 2,883 | 0.27 |
chr2_PATERNAL_Q | 5 | 1,104 | 1,390 | 3,549 | 3,861 | 4,318 | 0.52 |
chr3_MATERNAL_P | 10 | 1,572 | 2,203 | 2,917 | 5,385 | 6,438 | 0.5 |
chr3_MATERNAL_Q | 10 | 2,739 | 3,048 | 3,297 | 4,895 | 6,177 | 0.57 |
chr3_PATERNAL_P | 5 | 1,587 | 1,666 | 5,923 | 6,089 | 6,644 | 0.58 |
chr3_PATERNAL_Q | 5 | 1,449 | 1,790 | 3,098 | 3,813 | 4,708 | 0.46 |
chr4_MATERNAL_P | 10 | 1,589 | 2,910 | 4,167 | 5,040 | 5,328 | 0.34 |
chr4_MATERNAL_Q | 9 | 933 | 1,750 | 3,447 | 4,127 | 4,782 | 0.43 |
chr4_PATERNAL_P | 7 | 1,025 | 2,216 | 3,478 | 4,016 | 4,334 | 0.47 |
chr4_PATERNAL_Q | 10 | 3,987 | 4,698 | 7,009 | 7,583 | 8,007 | 0.26 |
chr5_MATERNAL_P | 13 | 1,575 | 2,216 | 3,136 | 5,020 | 6,528 | 0.43 |
chr5_MATERNAL_Q | 7 | 2,016 | 2,250 | 4,400 | 4,873 | 5,403 | 0.4 |
chr5_PATERNAL_P | 10 | 1,609 | 2,224 | 2,655 | 3,975 | 5,974 | 0.47 |
chr5_PATERNAL_Q | 11 | 1,127 | 1,797 | 2,303 | 3,397 | 5,127 | 0.47 |
chr6_MATERNAL_P | 13 | 937 | 1,289 | 2,046 | 3,618 | 4,502 | 0.53 |
chr6_MATERNAL_Q | 13 | 104 | 1,532 | 2,156 | 2,822 | 4,259 | 0.65 |
chr6_PATERNAL_P | 11 | 2,149 | 3,139 | 3,795 | 4,303 | 5,021 | 0.26 |
chr6_PATERNAL_Q | 9 | 1,362 | 1,984 | 2,758 | 3,096 | 4,565 | 0.41 |
chr7_MATERNAL_P | 13 | 1,219 | 1,829 | 3,104 | 4,111 | 4,401 | 0.43 |
chr7_MATERNAL_Q | 13 | 839 | 1,309 | 1,439 | 2,258 | 3,529 | 0.53 |
chr7_PATERNAL_P | 16 | 886 | 1,587 | 2,099 | 4,009 | 4,752 | 0.95 |
chr7_PATERNAL_Q | 13 | 947 | 1,367 | 2,320 | 2,501 | 2,858 | 0.36 |
chr8_MATERNAL_P | 10 | 1,280 | 2,348 | 3,888 | 4,914 | 8,036 | 0.51 |
chr8_MATERNAL_Q | 12 | 1,516 | 1,931 | 2,234 | 2,988 | 4,449 | 0.48 |
chr8_PATERNAL_P | 7 | 1,606 | 1,757 | 1,965 | 3,597 | 4,291 | 0.43 |
chr8_PATERNAL_Q | 1 | 970 | 970 | 970 | 970 | 970 | 0.0 |
chr9_MATERNAL_P | 2 | 3,232 | 3,482 | 3,732 | 3,982 | 4,232 | 0.19 |
chr9_MATERNAL_Q | 4 | 1,905 | 2,405 | 2,803 | 3,689 | 3,035 | 0.5 |
chr9_PATERNAL_P | 10 | 1,318 | 1,807 | 2,343 | 3,044 | 4,388 | 0.45 |
chr9_PATERNAL_Q | 8 | 1,848 | 1,978 | 2,774 | 3,532 | 4,098 | 0.31 |
chr10_MATERNAL_P | 6 | 1,744 | 3,756 | 5,323 | 7,239 | 7,593 | 0.45 |
chr10_MATERNAL_Q | 7 | 652 | 1,391 | 1,450 | 2,481 | 3,410 | 0.64 |
chr10_PATERNAL_P | 7 | 1,594 | 1,954 | 2,437 | 4,755 | 7,023 | 0.6 |
chr10_PATERNAL_Q | 8 | 4,162 | 3,481 | 4,438 | 4,670 | 4,970 | 0.39 |
chr11_MATERNAL_P | 6 | 2,762 | 3,033 | 3,851 | 4,436 | 5,129 | 0.25 |
chr11_MATERNAL_Q | 5 | 1,702 | 1,908 | 2,227 | 4,123 | 4,433 | 0.45 |
chr11_PATERNAL_P | 5 | 1,940 | 1,953 | 3,305 | 3,342 | 3,895 | 0.31 |
chr11_PATERNAL_Q | 7 | 2,055 | 2,121 | 2,271 | 2,957 | 3,538 | 0.42 |
chr12_MATERNAL_P | 15 | 1,186 | 1,545 | 1,833 | 4,332 | 5,423 | 0.67 |
chr12_MATERNAL_Q | 15 | 1,168 | 1,508 | 1,587 | 3,273 | 3,986 | 0.47 |
chr12_PATERNAL_P | 8 | 2,366 | 2,570 | 3,458 | 4,907 | 6,092 | 0.37 |
chr12_PATERNAL_Q | 7 | 3,459 | 3,600 | 4,084 | 5,526 | 7,766 | 0.37 |
chr13_22_PATERNAL_P | 8 | 1,904 | 2,558 | 3,816 | 4,891 | 5,290 | 0.38 |
chr13_MATERNAL_P | 10 | 1,994 | 2,600 | 2,895 | 5,239 | 6,764 | 0.5 |
chr13_MATERNAL_Q | 5 | 5,232 | 5,232 | 5,403 | 5,507 | 5,597 | 0.37 |
chr13_PATERNAL_Q | 8 | 1,990 | 2,386 | 2,746 | 6,501 | 11,807 | 0.79 |
chr14_MATERNAL_P | 4 | 1,136 | 1,158 | 1,246 | 1,816 | 1,327 | 0.6 |
chr14_MATERNAL_Q | 10 | 4,127 | 5,474 | 6,288 | 6,862 | 7,415 | 0.31 |
chr14_PATERNAL_P | 10 | 1,628 | 2,632 | 4,247 | 5,561 | 6,445 | 0.46 |
chr14_PATERNAL_Q | 10 | 1,204 | 1,569 | 1,718 | 4,146 | 5,237 | 0.6 |
chr15_MATERNAL_P | 6 | 2,226 | 2,692 | 3,102 | 4,773 | 7,169 | 0.49 |
chr15_MATERNAL_Q | 9 | 1,351 | 1,674 | 2,173 | 4,563 | 5,167 | 0.53 |
chr15_PATERNAL_P | 12 | 1,819 | 2,389 | 2,545 | 3,571 | 4,017 | 0.35 |
chr15_PATERNAL_Q | 4 | 3,696 | 3,792 | 5,243 | 6,808 | 7,249 | 0.35 |
chr16_MATERNAL_P | 5 | 1,675 | 2,208 | 2,700 | 3,117 | 3,117 | 0.48 |
chr16_MATERNAL_Q | 7 | 1,409 | 2,497 | 3,286 | 3,317 | 3,443 | 0.27 |
chr16_PATERNAL_P | 8 | 1,568 | 2,416 | 4,720 | 5,469 | 7,715 | 0.49 |
chr16_PATERNAL_Q | 7 | 5,622 | 5,749 | 6,318 | 7,001 | 8,334 | 0.34 |
chr17_MATERNAL_P | 6 | 1,360 | 1,711 | 2,608 | 2,914 | 4,293 | 0.43 |
chr17_MATERNAL_Q | 12 | 1,333 | 1,562 | 1,767 | 2,920 | 3,959 | 0.43 |
chr17_PATERNAL_P | 7 | 2,528 | 3,136 | 3,707 | 5,974 | 6,009 | 0.36 |
chr17_PATERNAL_Q | 9 | 1,076 | 1,728 | 1,917 | 2,270 | 2,822 | 0.34 |
chr18_MATERNAL_P | 8 | 1,283 | 1,719 | 2,481 | 3,483 | 5,993 | 0.57 |
chr18_MATERNAL_Q | 7 | 4,324 | 5,411 | 6,125 | 7,465 | 8,704 | 0.27 |
chr18_PATERNAL_P | 5 | 2,068 | 3,336 | 5,507 | 6,661 | 7,937 | 0.47 |
chr18_PATERNAL_Q | 11 | 5,922 | 6,042 | 6,654 | 8,621 | 9,339 | 0.43 |
chr19_MATERNAL_P | 5 | 1,568 | 1,763 | 2,197 | 4,032 | 5,168 | 0.54 |
chr19_MATERNAL_Q | 7 | 1,942 | 2,093 | 2,128 | 2,298 | 2,558 | 0.09 |
chr19_PATERNAL_P | 7 | 876 | 1,874 | 2,713 | 2,760 | 3,887 | 0.44 |
chr19_PATERNAL_Q | 13 | 1,877 | 2,753 | 3,384 | 5,514 | 6,918 | 0.42 |
chr20_MATERNAL_P | 13 | 1,565 | 2,427 | 3,142 | 3,867 | 4,208 | 0.27 |
chr20_MATERNAL_Q | 11 | 1,059 | 2,282 | 2,806 | 5,718 | 6,596 | 0.54 |
chr20_PATERNAL_P | 12 | 736 | 1,054 | 1,782 | 2,658 | 2,982 | 0.47 |
chr20_PATERNAL_Q | 9 | 1,650 | 2,678 | 4,036 | 4,525 | 5,141 | 0.34 |
chr21_MATERNAL_P | 4 | 782 | 1,124 | 1,767 | 2,691 | 3,873 | 0.67 |
chr21_MATERNAL_Q | 9 | 1,248 | 1,958 | 2,441 | 2,782 | 2,919 | 0.39 |
chr21_PATERNAL_P | 3 | 1,212 | 3,873 | 6,535 | 6,949 | 7,364 | 0.66 |
chr21_PATERNAL_Q | 6 | 1,892 | 2,085 | 2,158 | 2,348 | 2,405 | 0.37 |
chr22_MATERNAL_P | 1 | 1,967 | 1,967 | 1,967 | 1,967 | 1,967 | 0.0 |
chr22_MATERNAL_Q | 5 | 2,431 | 2,830 | 3,281 | 5,846 | 6,210 | 0.43 |
chr22_PATERNAL_Q | 8 | 1,813 | 2,202 | 4,024 | 4,498 | 5,259 | 0.39 |
chrX_MATERNAL_P | 7 | 698 | 932 | 1,416 | 2,830 | 4,414 | 0.8 |
chrX_MATERNAL_Q | 8 | 904 | 1,191 | 2,591 | 3,704 | 4,562 | 1.07 |
chrY_PATERNAL_P | 5 | 692 | 998 | 1,485 | 1,594 | 1,826 | 0.35 |
chrY_PATERNAL_Q | 9 | 2,191 | 2,995 | 3,554 | 4,772 | 5,476 | 0.33 |
Aligned telomere length boxplots
Boxplot displaying aggregated lengths for telomeres grouped by alignment target contig. Only primary alignments from reads which passed the QC filtering stages above are considered. Supplementary and secondary alignments for reads are not included.