BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525078.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 = 4,784,892 number of mapped reads = 4,303,642 (89.94%) number of supplementary alignments = 19,217 (0.4%) number of secondary alignments = 0 number of mapped bases = 249,000,982 bp number of sequenced bases = 248,936,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 295,586 duplication rate = 5.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6985 >>>>>>> ACTG content number of A's = 65,348,231 bp (26.25%) number of C's = 47,248,212 bp (18.98%) number of T's = 78,713,300 bp (31.62%) number of G's = 57,619,311 bp (23.15%) number of N's = 7,419 bp (0%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,205,195 number of insertions = 16,011 mapped reads with insertion percentage = 0.37% number of deletions = 38,892 mapped reads with deletion percentage = 0.9% homopolymer indels = 41.29% >>>>>>> Coverage mean coverageData = 0.0804X std coverageData = 0.6355X There is a 6.27% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 19908288 0.07987257131046425 1.3152166439358262 chr2 243199373 21055490 0.08657707353546508 0.6654955592855504 chr3 198022430 16817730 0.084928409372615 0.35917700015359366 chr4 191154276 16303116 0.08528773899883882 0.4268717596881532 chr5 180915260 15380058 0.08501249701103157 0.36837623926932417 chr6 171115067 14533643 0.08493491107945508 0.4239025308019984 chr7 159138663 13624725 0.08561542960807708 0.6784523610287826 chr8 146364022 12846093 0.08776810601720142 0.8064267621706671 chr9 141213431 10557510 0.07476278938368122 0.5954988355674453 chr10 135534747 11780872 0.08692141506708977 0.5875223751306641 chr11 135006516 11265240 0.0834421947456225 0.574554873217669 chr12 133851895 11194935 0.08363673147847477 0.379083207627595 chr13 115169878 7901947 0.06861123009959254 0.3238152774039745 chr14 107349540 7512374 0.06998049549164347 0.39128066994565464 chr15 102531392 7075396 0.06900711930254493 0.3263114416329078 chr16 90354753 7005053 0.07752832880855753 0.3872936848206934 chr17 81195210 6484379 0.0798615952837612 0.40128289450242355 chr18 78077248 6744329 0.08638020899507114 1.0916610304830303 chr19 59128983 4678629 0.0791258155074306 0.9023875537993971 chr20 63025520 5234700 0.0830568315818735 0.3800801170151551 chr21 48129895 3293339 0.06842605827417658 0.3905236483942386 chr22 51304566 2773620 0.05406185484543422 0.28490980853050046 chrMT 16571 10041 0.6059380846056364 0.8932858119824161 chrX 155270560 14310928 0.09216768458875912 0.467799053295426 chrY 59373566 708547 0.011933711375867167 0.27190890173788457