European Genome-Phenome Archive

File Quality

File InformationEGAF00002483921

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.

397 558206 911146 254119 252100 42790 18581 95775 55272 57068 36664 19562 59259 81155 12252 59448 75546 00943 00540 89938 15436 32534 09031 65428 47227 19725 57723 35522 34520 52919 40917 97716 46615 29213 89113 19012 00311 31410 5529 6278 9688 4458 0427 0766 8396 1625 7895 4655 2814 8354 3684 0063 7023 5773 3893 1412 9012 7172 6292 3952 0672 0002 0021 9501 7541 7371 6171 4421 3411 3391 3031 1991 1059979778841 0368558378107857676966596496266296115375294715115394785344654254514144304314554873663904654193563793523553933933303843343443513183383413482793133323052812603043213063252912522942592772832562322722672922952712812583022562542462492462672552502662412262562402382092382662761932502232622752431872032222441882072181821692071741571511521681521411571501551371431061171241181129910010911611111488881068583116927810392857959675773625879626959626683686763603970645461575355525243375348456241443546444848292338352933202625272437392339352433353628253030283226282932232227242630322624182037262019332630262522161192218231418221516161920171817811119451181151113871086101110668104571491177366758101069225547414234563774413223433412113321121151113212112332311431372241551212344111121491131522524312243312243311452322241412421113313433211323111212112121113132112254424311111321211312111111112123311461413132211121211221112111211111112211122112221111111132213212335313345553525123553311111442212222533314232915315152424422646134135131641127362412255224211154335125433171532123321444235141215123211221143114424121126311212221123131421111212332231131242311331241111133422111312315321121322132411122142224333122231314113607100200300400500600700800900>1000Coverage value1210201002001k2k10k20k100k200k# 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.

11 1570000000000000250 172227 8191 303 86200000000001 123 81657 8320497 362702 219169 156233 9661 615 8414 292 1191 885 9291 412 4923 360 14615 598 63535 935 12700510152025303540Phred quality score0M5M10M15M20M25M30M35M# 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).

55.5 %508 62455.5 %44.5 %

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.

52.2 %478 27652.2 %47.8 %

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%).

6 %30 3486 %94 %

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.

50 %457 85150 %50 %

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.

46.8 %428 40046.8 %53.2 %

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.

3.8 %34 8533.8 %96.2 %

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.

462 1861 322575421181167883832 3984512 6981 1731363223 8573071 8341 5942892 412579487 921122 00421521651 4291116142628463 01772 644140342462222855254882 244110198130322641861722446241 666288 060051015202530354045505560Phred quality score50k100k150k200k250k300k350k400k450k# 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.

92.68%94.14%95.69%94.25%95.38%95.03%93.05%94.28%93.91%94.2%96.18%94.37%96.77%93.82%92.92%94.21%93.37%95.33%92.25%95.84%93.23%95.25%99.05%98.61%7.32%5.86%4.31%5.75%4.62%4.97%6.95%5.72%6.09%5.8%3.82%5.63%3.23%6.18%7.08%5.79%6.63%4.67%7.75%4.16%6.77%4.75%0.95%1.39%123456789101112131415161718192021XYM0%10%20%30%40%50%60%70%80%90%100%mappedunmapped