BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068111.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 4,309,051 number of mapped reads = 3,646,913 (84.63%) number of supplementary alignments = 22,647 (0.53%) number of secondary alignments = 0 number of mapped bases = 242,603,558 bp number of sequenced bases = 242,493,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,306 duplication rate = 8.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.638 >>>>>>> ACTG content number of A's = 67,438,693 bp (27.81%) number of C's = 43,798,286 bp (18.06%) number of T's = 78,443,027 bp (32.35%) number of G's = 52,784,145 bp (21.77%) number of N's = 29,240 bp (0.01%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,327,658 number of insertions = 16,872 mapped reads with insertion percentage = 0.46% number of deletions = 61,987 mapped reads with deletion percentage = 1.68% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.0784X std coverageData = 0.8017X There is a 5.86% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 22620054 0.09075224731335775 1.9779164164184335 chr2 243199373 21847775 0.08983483275674399 0.7665515018269342 chr3 198022430 16612540 0.08389221362448689 0.3645503112378968 chr4 191154276 16600259 0.08684220592585645 0.3976074779481683 chr5 180915260 14665381 0.08106215584025361 0.3619950431187277 chr6 171115067 17998081 0.10518115859429257 0.4792265799274768 chr7 159138663 20138407 0.12654628749771513 0.7491996023667884 chr8 146364022 7112368 0.04859369059972949 1.2493941587659145 chr9 141213431 9739283 0.06896853175389528 0.6127608524464776 chr10 135534747 12617405 0.09309350760067453 0.6012738709676679 chr11 135006516 7126552 0.05278672623475448 0.41199224288038827 chr12 133851895 9840203 0.07351560469128958 0.37428084253834587 chr13 115169878 7424697 0.0644673514371527 0.32518241102585205 chr14 107349540 3370299 0.03139556070757266 0.3008123563042921 chr15 102531392 3769498 0.036764330674453345 0.2620997357391797 chr16 90354753 6022133 0.06664987507630063 0.37200863300003817 chr17 81195210 5281396 0.06504565971317766 0.36278409842951853 chr18 78077248 7177570 0.09192908541038741 0.9850308851261205 chr19 59128983 4826442 0.08162565556048884 1.2625366432041818 chr20 63025520 3446640 0.05468641908864853 0.32085063110321 chr21 48129895 2672091 0.05551832182472037 0.32879427060239363 chr22 51304566 1539155 0.03000035123579449 0.2133076856047613 chrMT 16571 168755 10.183754752278077 6.932601685287326 chrX 155270560 19335956 0.12453072881298297 0.520741078973098 chrY 59373566 650618 0.010958041496109565 0.3606699764676317