BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716752.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,665,886 number of mapped reads = 1,517,148 (91.07%) number of supplementary alignments = 6,620 (0.4%) number of secondary alignments = 0 number of mapped bases = 87,951,001 bp number of sequenced bases = 87,929,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,672 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3458 >>>>>>> ACTG content number of A's = 22,537,872 bp (25.63%) number of C's = 16,843,532 bp (19.16%) number of T's = 27,768,885 bp (31.58%) number of G's = 20,776,704 bp (23.63%) number of N's = 2,062 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 416,649 number of insertions = 5,592 mapped reads with insertion percentage = 0.37% number of deletions = 12,997 mapped reads with deletion percentage = 0.85% homopolymer indels = 40.66% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2319X There is a 2.54% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 9900494 0.039721040454298404 0.3684068891016866 chr2 243199373 7326506 0.030125513522602707 0.25866025715712976 chr3 198022430 5845943 0.029521620353815475 0.18791697683981728 chr4 191154276 5681385 0.029721464352699074 0.20126296755440118 chr5 180915260 4392299 0.024278211799270002 0.17254633702279262 chr6 171115067 4679464 0.027346884655107546 0.1946925516956619 chr7 159138663 3806697 0.023920629520432755 0.20749389557666562 chr8 146364022 5487920 0.03749500679887029 0.24875112899254917 chr9 141213431 3207881 0.02271654315941095 0.2243080673159394 chr10 135534747 4170264 0.030768965835749854 0.22945192073467344 chr11 135006516 2717895 0.020131583871107375 0.20772844920136638 chr12 133851895 3920454 0.02928949194182122 0.18974248497016336 chr13 115169878 2755975 0.02392965111936647 0.16810855355096108 chr14 107349540 3141382 0.029263115612791633 0.19933522805945517 chr15 102531392 2525549 0.02463195857128322 0.1718880570964811 chr16 90354753 2530559 0.02800692731681752 0.19298246651690684 chr17 81195210 1928106 0.02374654859566223 0.17365829450735804 chr18 78077248 2160353 0.027669430664359482 0.4248964726224375 chr19 59128983 1619027 0.027381275947194965 0.2645610805496384 chr20 63025520 2712925 0.04304486500071717 0.23176759327528682 chr21 48129895 1174857 0.02441013012806282 0.18458639889361436 chr22 51304566 1033794 0.02015013634458968 0.15475962848590438 chrMT 16571 2509 0.15140908816607326 0.4109432855294879 chrX 155270560 4996165 0.03217715579824018 0.21928639625089746 chrY 59373566 232598 0.003917534614646525 0.08982354808099122