BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013202.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 = 2,261,259 number of mapped reads = 1,941,556 (85.86%) number of supplementary alignments = 11,387 (0.5%) number of secondary alignments = 0 number of mapped bases = 130,789,302 bp number of sequenced bases = 130,738,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,937 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5505 >>>>>>> ACTG content number of A's = 36,025,137 bp (27.56%) number of C's = 24,438,728 bp (18.69%) number of T's = 41,315,731 bp (31.6%) number of G's = 28,931,255 bp (22.13%) number of N's = 27,647 bp (0.02%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,018,716 number of insertions = 9,247 mapped reads with insertion percentage = 0.47% number of deletions = 29,162 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3601X There is a 3.17% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 8299879 0.03329933127829599 0.44085923306191516 chr2 243199373 24149203 0.09929796570651521 0.5684887029068666 chr3 198022430 6547595 0.03306491592896825 0.23065214082482516 chr4 191154276 11774859 0.06159872144319701 0.33339391258146955 chr5 180915260 11814837 0.06530591725651004 0.32507707526298274 chr6 171115067 6285871 0.03673476047553428 0.27111317427982373 chr7 159138663 3589412 0.022555247934940865 0.5797383923071777 chr8 146364022 5905951 0.040351111696015025 0.4243281706935665 chr9 141213431 6581488 0.04660667157077998 0.3462041016466454 chr10 135534747 6199609 0.045741842127022966 0.38906414160102387 chr11 135006516 3062987 0.02268769753305833 0.22041628254267628 chr12 133851895 7927416 0.059225280299543014 0.31738742848240536 chr13 115169878 554870 0.004817839609068614 0.0827236998271785 chr14 107349540 4678330 0.04358034510441312 0.2844599578646517 chr15 102531392 2626602 0.025617539650685715 0.2019462741020696 chr16 90354753 3618523 0.040047954090472695 0.26380765404513684 chr17 81195210 4229178 0.05208654549942047 0.3618701312779357 chr18 78077248 1702582 0.021806378216609273 0.4375922809766363 chr19 59128983 1717862 0.02905279125128873 0.38031363394686934 chr20 63025520 1819043 0.0288620070092242 0.22147763269500068 chr21 48129895 1253288 0.02603969944251904 0.233912963264037 chr22 51304566 328165 0.00639640923967664 0.09301098735153228 chrMT 16571 26697 1.6110675276084727 1.7119391190639397 chrX 155270560 5817891 0.037469376036255685 0.2596018310186898 chrY 59373566 277164 0.004668138006061485 0.13855875884873523