BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238043.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 = 2,159,786 number of mapped reads = 1,845,333 (85.44%) number of supplementary alignments = 18,408 (0.85%) number of secondary alignments = 0 number of mapped bases = 122,183,943 bp number of sequenced bases = 122,119,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,730 duplication rate = 7.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6712 >>>>>>> ACTG content number of A's = 35,005,624 bp (28.67%) number of C's = 22,714,911 bp (18.6%) number of T's = 38,333,312 bp (31.39%) number of G's = 25,827,038 bp (21.15%) number of N's = 238,250 bp (0.2%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,150,536 number of insertions = 10,584 mapped reads with insertion percentage = 0.57% number of deletions = 39,421 mapped reads with deletion percentage = 2.11% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0395X std coverageData = 0.5052X There is a 2.27% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 10662631 0.04277875399957379 1.1745515703830394 chr2 243199373 10890962 0.0447820315720962 0.4877050196550437 chr3 198022430 6801743 0.034348346295922136 0.2928725490622277 chr4 191154276 8318578 0.04351761401351022 0.3429530305954235 chr5 180915260 7902815 0.04368241241783584 0.3306241676560496 chr6 171115067 7560152 0.04418168506458873 0.3536448308811257 chr7 159138663 7192467 0.04519622613644806 0.5579350211559924 chr8 146364022 4986277 0.03406764129507182 0.5671176256036777 chr9 141213431 4762404 0.03372486573178723 0.37209117506855627 chr10 135534747 5654589 0.04172058549679515 0.3989515582122057 chr11 135006516 5820973 0.04311623744145801 0.37610533666498047 chr12 133851895 5421969 0.04050722628917581 0.3221670258893605 chr13 115169878 4461427 0.038737793922122586 0.31356865488444646 chr14 107349540 3136376 0.02921648290248845 0.274781331846166 chr15 102531392 3945395 0.03847987355911446 0.30911490140054493 chr16 90354753 3205617 0.03547812255100736 0.3059831449400854 chr17 81195210 3021598 0.03721399328852035 0.31909107695730393 chr18 78077248 3818893 0.04891172649937662 0.6375409890074547 chr19 59128983 2197739 0.03716855742301538 0.6598180961663785 chr20 63025520 2547130 0.04041426393625947 0.32517858059735977 chr21 48129895 1533548 0.031862691576617815 0.29169203235951685 chr22 51304566 1614352 0.03146604924013976 0.27388409039383466 chrMT 16571 37124 2.2402993180858126 2.5519053372160183 chrX 155270560 6340034 0.0408321706317025 0.336217968969699 chrY 59373566 349150 0.005880563077515001 0.14161694362877986