BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068099.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 = 2,607,834 number of mapped reads = 2,368,810 (90.83%) number of supplementary alignments = 18,745 (0.72%) number of secondary alignments = 0 number of mapped bases = 157,724,892 bp number of sequenced bases = 157,651,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,655 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1077 >>>>>>> ACTG content number of A's = 43,752,643 bp (27.75%) number of C's = 29,170,225 bp (18.5%) number of T's = 49,612,173 bp (31.47%) number of G's = 35,113,154 bp (22.27%) number of N's = 3,317 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,261,923 number of insertions = 12,370 mapped reads with insertion percentage = 0.52% number of deletions = 44,010 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.5084X There is a 4.17% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 24362683 0.0977437203656957 1.1564020357605311 chr2 243199373 23567715 0.0969069727001311 0.6217024451803483 chr3 198022430 6076775 0.030687306483412006 0.22896894943548976 chr4 191154276 7961408 0.04164912324535183 0.2532515502489787 chr5 180915260 6319286 0.03492953551845212 0.22106529247804563 chr6 171115067 3151176 0.01841553789065226 0.1763659470492759 chr7 159138663 5351474 0.03362774261839815 0.26056520579805786 chr8 146364022 7446181 0.05087439452845864 0.46388782455075495 chr9 141213431 10954117 0.07757135367669099 0.5294724094408734 chr10 135534747 11073103 0.08169936673139619 0.6975497212452536 chr11 135006516 5704411 0.04225285689173699 0.3231291983900452 chr12 133851895 5661033 0.04229326002444717 0.2596844182256315 chr13 115169878 6506567 0.056495388490382874 0.2758352304736002 chr14 107349540 3587608 0.03341987306140296 0.2642907523400963 chr15 102531392 2851584 0.027811813966204614 0.19842441720627918 chr16 90354753 5524951 0.06114732005299157 0.3674255978535189 chr17 81195210 6431354 0.07920853951852579 0.3391684512276903 chr18 78077248 1633272 0.020918667625170397 0.7710559553207861 chr19 59128983 2400476 0.040597282046944724 0.935934789892957 chr20 63025520 2779798 0.04410591138319842 0.2597860163353875 chr21 48129895 944760 0.01962938003500735 0.20007533522047272 chr22 51304566 3278358 0.06389992656793939 0.29457942669241993 chrMT 16571 61481 3.7101562971456157 2.996098971417657 chrX 155270560 3586487 0.023098306594630687 0.21451030628041368 chrY 59373566 508834 0.008570042769538214 0.2813927830995138