BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716798.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 = 832,062 number of mapped reads = 632,699 (76.04%) number of supplementary alignments = 735 (0.09%) number of secondary alignments = 0 number of mapped bases = 33,487,870 bp number of sequenced bases = 33,479,008 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,370 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8956 >>>>>>> ACTG content number of A's = 6,981,174 bp (20.85%) number of C's = 6,250,135 bp (18.67%) number of T's = 10,781,828 bp (32.2%) number of G's = 9,465,324 bp (28.27%) number of N's = 547 bp (0%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 224,095 number of insertions = 1,827 mapped reads with insertion percentage = 0.29% number of deletions = 5,278 mapped reads with deletion percentage = 0.83% homopolymer indels = 39.76% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1244X There is a 0.98% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3270546 0.01312151595401642 0.1524218754049087 chr2 243199373 2905243 0.011945931291525163 0.1597114846618887 chr3 198022430 2294141 0.011585258296244521 0.11761508067243484 chr4 191154276 2158737 0.011293166154441661 0.12039060772111622 chr5 180915260 2061486 0.011394760176670559 0.1162353070243663 chr6 171115067 1406668 0.008220596962393733 0.10850059167114262 chr7 159138663 1887024 0.01185773440863959 0.1326872779955785 chr8 146364022 2079551 0.01420807498717137 0.1321634952308616 chr9 141213431 1477963 0.010466164510938056 0.11551037025783979 chr10 135534747 1743553 0.01286425096584273 0.14109983522623717 chr11 135006516 1413114 0.010467005903626163 0.12018321886833258 chr12 133851895 1648068 0.012312623590424327 0.12163085929645469 chr13 115169878 583834 0.005069328978537253 0.07849124305356703 chr14 107349540 1072267 0.009988557007323925 0.10923121376323286 chr15 102531392 680576 0.006637732958897115 0.0891537540753578 chr16 90354753 907687 0.010045813527928077 0.11523258750502399 chr17 81195210 1296981 0.01597361469968487 0.1417048054617229 chr18 78077248 869758 0.011139711276708934 0.12870585393560113 chr19 59128983 911225 0.01541080116328062 0.16052536179551752 chr20 63025520 868064 0.013773214405847028 0.13008775320903676 chr21 48129895 450679 0.009363806008718698 0.109383707085654 chr22 51304566 375037 0.007310012134202636 0.09445901954320723 chrMT 16571 1403 0.08466598274093295 0.31075249443945296 chrX 155270560 1024680 0.006599319278554801 0.090626840987055 chrY 59373566 99585 0.0016772615611465884 0.060270032313256595