BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524951.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 = 968,497 number of mapped reads = 895,992 (92.51%) number of supplementary alignments = 2,220 (0.23%) number of secondary alignments = 0 number of mapped bases = 52,300,146 bp number of sequenced bases = 52,282,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,151 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5029 >>>>>>> ACTG content number of A's = 13,874,301 bp (26.54%) number of C's = 9,672,204 bp (18.5%) number of T's = 15,808,285 bp (30.24%) number of G's = 12,927,325 bp (24.73%) number of N's = 726 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 258,120 number of insertions = 3,823 mapped reads with insertion percentage = 0.42% number of deletions = 10,075 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.29% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1776X There is a 1.58% 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 5612285 0.022516633970592996 0.30924581489880915 chr2 243199373 4991764 0.020525398311779363 0.2054246598336196 chr3 198022430 2884700 0.014567541666870768 0.1270700189228663 chr4 191154276 3401752 0.01779584569690714 0.14667387759262188 chr5 180915260 2258083 0.01248144020576263 0.1179682132971606 chr6 171115067 3517153 0.02055431506800041 0.1832730151695793 chr7 159138663 3319058 0.020856389876795684 0.24183789096578934 chr8 146364022 3176158 0.02170040120925346 0.17888911490247755 chr9 141213431 1466182 0.010382737602346055 0.13510161090308134 chr10 135534747 2625523 0.01937158594467292 0.17566069170204546 chr11 135006516 2212326 0.01638680906334921 0.16709935389699376 chr12 133851895 2827744 0.021125916820228807 0.15312230993923392 chr13 115169878 1018899 0.008846922630238438 0.09887034372990831 chr14 107349540 1206731 0.011241138061700125 0.1139772929545566 chr15 102531392 1453216 0.014173376286552318 0.1280336947472122 chr16 90354753 1663283 0.018408361981798568 0.14655440402618597 chr17 81195210 1340921 0.016514779628010075 0.15993116542990027 chr18 78077248 1023911 0.013114076459252253 0.20742275364991128 chr19 59128983 1269481 0.021469691098864326 0.20684396025406923 chr20 63025520 1255585 0.019921850704286138 0.14811954952899029 chr21 48129895 747108 0.015522743193185857 0.13334481129899237 chr22 51304566 687400 0.013398417598932618 0.12052866564680594 chrMT 16571 10073 0.6078691690302336 0.8358746868317533 chrX 155270560 2194742 0.01413495256280392 0.13644327574411702 chrY 59373566 136068 0.00229172692777119 0.06389916688063889