BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714201.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 107,214 number of mapped reads = 25,253 (23.55%) number of supplementary alignments = 835 (0.78%) number of secondary alignments = 0 number of mapped bases = 2,859,450 bp number of sequenced bases = 2,817,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,832 duplication rate = 49.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.1501 >>>>>>> ACTG content number of A's = 469,906 bp (16.68%) number of C's = 393,780 bp (13.97%) number of T's = 431,417 bp (15.31%) number of G's = 1,522,860 bp (54.04%) number of N's = 36 bp (0%) GC percentage = 68.01% >>>>>>> Mismatches and indels general error rate = 0.0361 number of mismatches = 91,636 number of insertions = 1,990 mapped reads with insertion percentage = 5.88% number of deletions = 5,513 mapped reads with deletion percentage = 21.26% homopolymer indels = 36.79% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 1.4337X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 55167 2.2133144454633075E-4 0.0912794206255338 chr2 243199373 1210206 0.004976188816078897 5.058672738398614 chr3 198022430 34986 1.7667695523178865E-4 0.046454421242090885 chr4 191154276 21781 1.1394461298893466E-4 0.03224498227593691 chr5 180915260 35443 1.9590939979303017E-4 0.05736680643241943 chr6 171115067 50540 2.953568080594563E-4 0.11794850729105794 chr7 159138663 69626 4.375178142598823E-4 0.2126241851571927 chr8 146364022 85301 5.828003278018693E-4 0.2995403331207094 chr9 141213431 18947 1.3417278983894954E-4 0.05506844659470605 chr10 135534747 24853 1.833699516183846E-4 0.09776055027412123 chr11 135006516 22520 1.66806763608358E-4 0.046747958939295196 chr12 133851895 32615 2.4366483567528124E-4 0.055690073213852165 chr13 115169878 7146 6.204747390632819E-5 0.016237843980019668 chr14 107349540 20445 1.904526092985587E-4 0.07744668647886213 chr15 102531392 17988 1.754389523942092E-4 0.04235767485585696 chr16 90354753 18010 1.9932543006343008E-4 0.06615955102343725 chr17 81195210 29854 3.676817881251862E-4 0.07407495522045965 chr18 78077248 7453 9.545674560660745E-5 0.022247175536401157 chr19 59128983 17552 2.968425822578413E-4 0.08242869622210508 chr20 63025520 48151 7.639921098627985E-4 0.2853062691348927 chr21 48129895 2680 5.568264796754699E-5 0.020807456944514958 chr22 51304566 6763 1.3182062586788085E-4 0.026647980276512273 chrMT 16571 0 0.0 0.0 chrX 155270560 1015752 0.006541819646944018 0.8170882221492803 chrY 59373566 5671 9.551388575852088E-5 0.02866595672126916