LQC: Long-read RNA-seq Quality Control
Please cite:
LQC is used to generate quality control summary report for mapped SAM/BAM files of long-read RNA-seq data (PacBio, Oxford Nanopore). LQC provides detailed information about the indels, mismatches and splicing sites in the BAM files, which provides a good reference for evaluation for the sequencing quality of the long-read sequencing data.
Guidance
- Click the contents on the left side of the page to switch to different sections.
-
The correct view of this page requires network
connection to bootstrap
(
).
- More figures for each chromosome are stored in the fig subdirectory under the output directory.
Read Statistic
Read count for each contig
Total read count for all the analyzed contigs is {%readstat_total_read_count%}.
Total base number for all the analyzed contigs is {%readstat_total_base%}.
The barplot shows the read count for each contig.
Histogram of length
The histogram shows the read length distribution for all the analyzed contigs.
The median of read length is {%readstat_median_read_length%}.
The mean of read length is {%readstat_mean_read_length%}.
Histogram of length by contig
The histogram shows the read length distribution for each analyzed contig.
Cumulative curve of length
N50 is the shortest read length with reads longer than N50 cover 50% of all the bases, which can assess the sequencing quality.
L50 is the rank of the N50 read (descendent rank by read length).
Cumulative curve of length by contig
N50 of reads
Read N50 for all the analyzed contigs is {%readstat_N50%}.
L50 of reads
Read L50 for all the analyzed contigs is {%readstat_L50%}.
Read ratio with elements
The ratio of reads with at least one element (insertion, deletion, mismatch) is calculated for all the analyzed contigs.
Read ratio with elements by contig
The ratio of reads with at least one element (insertion, deletion, mismatch) is calculated for each analyzed contig.
Elements per read per kb
The count of elements per read normalized by the read length. There are {%readstat_insertion_per_read_per_kb%} insertions, {%readstat_deletion_per_read_per_kb%} deletions, {%readstat_mismatch_per_read_per_kb%} mismatches per read per kb.
Elements per read per kb by contig
The count of elements per read normalized by the read length for each analyzed contig.
| Contig | Read count | Total base | Mean read length | Median read length | Read length N50 | Read length L50 |
|---|
Insertion
Count of insertion
The total number of insertions found in all the analyzed contigs is {%insertion_total_insertion_number%}.
The total number of bases inserted found in all the analyzed contigs is {%insertion_total_insertion_length%}.
Average number of insertions per read
The mean numbers of insertions found in reads are presented in the barplot.In average, {%insertion_mean_insertion_per_read_per_kb%} insertions can be found per read per kb.
Histogram of length
The histogram shows the insertion length distribution for all the analyzed contigs.
The median of insertion length is {%insertion_median_length%}.
The mean of insertion length is {%insertion_mean_length%}.
Histogram of length by contig
The histogram shows the insertion length distribution for each analyzed contig.
Histogram of read locations by contig
The histogram shows the read location of insertion for each analyzed contig.
| Contig | Total insertion count | Total insertion length | Mean insertion length | Median insertion length |
|---|
Deletion
Count of deletion
The total number of deletions found in all the analyzed contigs is {%deletion_total_deletion_number%}.
The total number of bases deleted found in all the analyzed contigs is {%deletion_total_deletion_length%}.
Average number of deletions per read
The mean numbers of deletions found in reads are presented in the barplot. In average, {%deletion_mean_deletion_per_read_per_kb%} deletions can be found per read per kb.
Histogram of length
The histogram shows the deletion length distribution for all the analyzed contigs.
The median of deletion length is {%deletion_median_length%}.
The mean of deletion length is {%deletion_mean_length%}.
Histogram of length by contig
The histogram shows the deletion length distribution for each analyzed contig.
Histogram of read locations by contig
The histogram shows the read location of deletion for each analyzed contig.
| Contig | Total deletion count | Total deletion length | Mean deletion length | Median deletion length |
|---|
Mismatch
Count of mismatch
The total number of mismatches found in all the analyzed contigs is {%mismatch_total_mismatch_number%}.
Average number of mismatchs per read
The mean numbers of mismatches found in reads are presented in the barplot. In average, {%mismatch_mean_mismatch_per_read_per_kb%} mismatches can be found per read per kb.
Mismatch types
The mismatch types are counted for all the analyzed contigs.
Mismatch types by contig
The mismatch types are counted for each analyzed contig.
Histogram of read locations by contig
The histogram shows the read location of mismatch for each analyzed contig.
| Contig | Relative location | Mismatch type | Counts |
|---|
Splicing
Count of intron
The total number of introns found in all the analyzed contigs is {%intron_total_intron_number%}.
Average number of introns per read
The mean numbers of introns found in reads are presented in the barplot. In average, {%intron_mean_intron_per_read%} introns can be found per read.
Splice sites types
The splice types are counted for all the analyzed contigs.
Splice sites types by contig
The intron types are counted for each analyzed contig.
| Contig | gt-ag | gt-ag % | gc-ag | gc-ag % | at-ac | at-ac % | Other | Other % |
|---|