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
Status definitions (in order of filtering):
  • 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.

Software versions

Name Version
pysam 0.22.1
pandas 2.2.2
numpy 1.26.4
edlib 1.3.9
scipy 1.15.2
samtools 1.21
minimap2 2.28-r1209
ezcharts (report) 0.14.0

Workflow parameters

Key Value
fastq test_data/HG002_small_test.fastq.gz
bam None
read_quality 9
out_dir wf-teloseq
min_length 100
sample None
sample_sheet None
analyse_unclassified False
store_dir wf-teloseq/store_dir
skip_mapping False
reference None
alignment_threads 2