European Genome-Phenome Archive

File Quality

File InformationEGAF00005114797

File Data

Base Coverage Distribution

This chart represents the base coverage distribution along the reference file. Y-axis represents the number of times a position in the reference file is covered. The x-axis represents the range of the values for the coverage.

Data is represented in a log scale to minimise the variability. A high peak in the beginning (low coverage) and a curve descending is expected.

73 608 51734 679 45620 018 81711 183 0695 809 3242 902 2421 405 108676 282326 773161 30784 02150 57131 31222 20316 15011 84810 1979 4288 0857 5847 3526 2226 2645 3024 6034 5434 0104 0253 9873 2303 1442 5782 8572 5922 3081 9942 3682 3942 1931 6881 9061 7941 4161 4681 3281 3401 3671 5071 1431 1711 2789711 0089401 1778559348961 00395486084670371872164977984966578468585067866055349053163849768550060245744150339640848252142041756239146848749338637837848038850340038951431339950036438535029833636834644834636841542340246042943541536932834945437430538634940836636440137939939137934536434642636629334934236630734529329431430230025928127626225822323020622123123121820129525422420121120816116219214416714614199115128111881138678801017666788885885862431008238336166577083505246419056395866584444435655393767673539526948365832333644353344393925284641363834532135172323312425284622332821254635291922122619192319181718251838312817221622251118142427131518171759242014151722191216232135232422312221193027344041363434302231382522192426212122302215242428263517223121222017142228211614202118222219322418273137283129242020312034351221212039362822192222181520233017262528221929248181925241718239212119171615142114161012139881671991614911152117201326151516151418251213321421201818161421241037241712413811811111720159712914104397128810106667111415881011101117111061113512971169781377448121575810838547107676776799421136857558588788118891681498116531644799812865755919761245106351093394561242233444337163335666625554441212645108519552643734423256453423543342811223341121216311122773215223136553678841426615751214393102233155262223364211233211122113112221321114112312221113112211311212232213223112221221112111121111113121236233121616221211143311232233111111211221111211111111111412484100200300400500600700800900>1000Coverage value1101001k10k100k1M10M# Bases

Base Quality

The base quality distribution shows the Phred quality scores describing the probability that a nucleotide has been incorrectly assigned; e.g. an error in the sequencing. Specifically, Q=-log10(P), where Q is the Phred score and P is the probability the nucleotide is wrong. The larger the score, the more confident we are in the base call. Depending on the sequencing technology, we can expect to see different distributions, but we expect to see a distribution skewed towards larger (more confident) scores; typically around 40.

009 211 84000000000012 182 120000000000000015 417 9260000000366 153 43300000000510152025303540Phred quality score0M50M100M150M200M250M300M350M# Bases

Mapped Reads

Number of reads successfully mapped (singletons & both mates) to the reference genome in the sample. Genetic variation, in particular structural variants, ensure that every sequenced sample is genetically different from the reference genome it was aligned to. Small differences against the reference are accepted, but, for more significant variation, the read can fail to be placed. Therefore, it is not expected that the mapped reads rate will hit 100%, but it is supposed to be high (usually >90%). Calculations are made taking into account the proportion of mapped reads against the total number of reads (mapped/mapped+unmapped).

78.8 %3 294 74278.8 %21.2 %

Both Mates Mapped

When working with paired-end sequencing, each DNA fragment is sequenced from both ends, creating two mates for each pair. This chart shows the fraction of reads in pairs where both of the mates successfully map to the reference genome. .

Notice that reads not mapped to the expected distance are also included as occurs with the proper pairs chart.

0 %00 %100 %

Singletons

When working with paired-end sequencing, each DNA fragment is sequenced from both ends, creating two mates for each pair. If one mate in the pair successfully maps to the reference genome, but the other is unmapped, the mapped mate is a singleton. One way in which a singleton could occur would be if the sample has a large insertion compared with the reference genome; one mate can fall in sequence flanking the insertion and will be mapped, but the other falls in the inserted sequence and so cannot map to the reference genome. There are unlikely to many such structural variants in the sample, or sequencing errors that would cause a read not to be able to map. Consequently, the singleton rate is expected to be very low (<1%).

100 %3 294 742100 %0 %

Forward Strand

Fraction of reads mapped to the forward DNA strand. The general expectation is that the DNA library preparation step will generate DNA from the forward and reverse strands in equal amounts so after mapping the reads to the reference genome, approximately 50% of them will consequently map to the forward strand. Deviations from the 50%, may be due to problems with the library preparation step.

100 %4 181 579100 %0 %

Proper Pairs

A fragment consisting of two mates is called a proper pair if both mates map to the reference genome at the expected distance according to the reference genome. In particular, if the DNA library consists of fragments ~500 base pairs in length, and 100 base pair reads are sequenced from either end, the expectation would be that the two reads map to the reference genome separated by ~300 base pairs. If the sequenced sample contains large structural variants, e.g. a large insertion, where we expect the reads mapping with a large separation would be a signal for this variant, and the reads would not be considered as proper pairs. Based on the sequencing technology, there is also an expectation of the orientation of each read in the fragment.

The rate of proper pairs is expected to be well over 90%; even if the mapping rate itself is low as a result of bacterial contamination, for example.

0 %00 %100 %

Duplicates

PCR duplicates are two (or more) reads that originate from the same DNA fragment. When sequencing data is analyzed, it is assumed that each observation (i.e. each read) is independent; an assumption that fails in the presence of duplicate reads. Typically, algorithms look for reads that map to the same genomic coordinate, and whose mates also map to identical genomic coordinates. It is important to note that as the sequencing depth increases, more reads are sampled from the DNA library, and consequently it is increasingly likely that duplicate reads will be sampled. As a result, the true duplicate rate is not independent of the depth, and they should both be considered when looking at the duplicate rate. Additionally, as the sequencing depth in increases, it is also increasingly likely that reads will map to the same location and be marked as duplicates, even when they are not. As such, as the sequencing depth approaches and surpasses the read length, the duplicate rate starts to become less indicative of problems.

39.7 %1 660 88239.7 %60.3 %

Mapping Quality Distribution

The mapping quality distribution shows the Phred quality scores describing the probability that a read does not map to the location that it has been assigned to (specifically, Q=-log10(P), where Q is the Phred score and P is the probability the read is in the wrong location). So the larger the score, the higher the quality of the mapping. Some scores have a specific meaning, e.g. a score of 0 means that the read could map equally to multiple places in the reference genome. The majority of reads should be well mapped, and so we expect to see this distribution heavily skewed to a significant value (typically around 60). It is not unusual to see some scores around zero. Reads originating from repetitive elements in the genome will plausibly map to multiple locations.

1 112 3995 7557 0456 2386 8178 4307 67310 49610 7958 77522 4642 3923 9112 0951 8363 5461 6431 8802 0502 3835 7882 6793 2126 1364 89118 51610 4462 2734 5772 1961 5845 5772 3515 3882 5462 1785 1004 30218 6892 4531 6935 3222 5626 0912 7101 5766 6001 8924 2195 1071 25314 9931 9233 5394 2939227 2261 2509207 6612 771 146051015202530354045505560Phred quality score0.2M0.4M0.6M0.8M1M1.2M1.4M1.6M1.8M2M2.2M2.4M2.6M# Reads

Mapped vs Unmapped

Stacked column chart for both mapped and unmapped reads along all chromosomes in the reference file. It is a similar representation as shown in the Mapped reads chart but for each chromosome. Although sequenced sample may be a female, it is possible to get reads in the Y chromosome as there are common regions in both chromosomes called pseudoautosomal regions (PAR1, PAR2).

Unmapped reads belonging to each chromosome are determined when the one mate/pair is aligned and the other is not. The unmapped read should have chromosome and POS identical to its mate. It could also be due when aligning is performed with bwa as it concatenates all the reference sequences together, so if a read hangs off of one reference onto another, it will be given the right chromosome and position, but it also be classified as unmapped.

100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%100%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%0%123456789101112131415161718192021XYM0%10%20%30%40%50%60%70%80%90%100%mappedunmapped