BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716583.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 = 2,201,601 number of mapped reads = 1,942,936 (88.25%) number of supplementary alignments = 7,226 (0.33%) number of secondary alignments = 0 number of mapped bases = 110,671,427 bp number of sequenced bases = 110,639,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,949 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1859 >>>>>>> ACTG content number of A's = 27,137,992 bp (24.53%) number of C's = 20,870,994 bp (18.86%) number of T's = 33,730,222 bp (30.49%) number of G's = 28,899,515 bp (26.12%) number of N's = 741 bp (0%) GC percentage = 44.98% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 586,167 number of insertions = 7,847 mapped reads with insertion percentage = 0.4% number of deletions = 20,003 mapped reads with deletion percentage = 1.02% homopolymer indels = 38.74% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.2872X There is a 3.18% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9327461 0.03742201709499452 0.364009606969725 chr2 243199373 8676497 0.035676477669208465 0.4399973215705884 chr3 198022430 6368943 0.03216273530225844 0.20182953238490034 chr4 191154276 6697458 0.03503692483447245 0.22642371703883618 chr5 180915260 6254848 0.03457335771454547 0.20310185841226944 chr6 171115067 5872026 0.03431624171353654 0.2417299446200833 chr7 159138663 6359481 0.03996188531507268 0.4257603503098151 chr8 146364022 5692274 0.03889121057359301 0.27605219429242817 chr9 141213431 3683323 0.02608337587945158 0.2118138070417668 chr10 135534747 4913468 0.03625246004258967 0.3630634205153043 chr11 135006516 3915695 0.02900374823390006 0.24462056644564217 chr12 133851895 5591651 0.041774910993975845 0.22725466559131544 chr13 115169878 3307094 0.0287149214484711 0.18598938756471292 chr14 107349540 3713382 0.0345915036058841 0.21314055976285337 chr15 102531392 4064185 0.03963844556016561 0.22334263045994943 chr16 90354753 3916933 0.04335060270708725 0.25045711989765745 chr17 81195210 5002871 0.061615346521057095 0.29273765532337187 chr18 78077248 2044379 0.026184055565073194 0.3372506452204506 chr19 59128983 2997235 0.050689777634091895 0.34259968110758415 chr20 63025520 3555123 0.05640767422466328 0.27831993742141903 chr21 48129895 1386165 0.028800499149229393 0.20287029049455876 chr22 51304566 1029853 0.020073320569557105 0.15627138498911788 chrMT 16571 9277 0.5598334439683785 0.9164461591830633 chrX 155270560 5953913 0.03834540817009999 0.23395656506094983 chrY 59373566 337892 0.005690950077009017 0.1566197823168327