BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716836.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 = 630,135 number of mapped reads = 550,871 (87.42%) number of supplementary alignments = 3,334 (0.53%) number of secondary alignments = 0 number of mapped bases = 32,534,033 bp number of sequenced bases = 32,524,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,434 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.328 >>>>>>> ACTG content number of A's = 8,188,698 bp (25.18%) number of C's = 6,411,010 bp (19.71%) number of T's = 10,065,716 bp (30.95%) number of G's = 7,859,272 bp (24.16%) number of N's = 197 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 161,850 number of insertions = 2,471 mapped reads with insertion percentage = 0.45% number of deletions = 5,592 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.05% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 0.1276X There is a 0.95% 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 2683167 0.010764936068103116 0.16067028802880703 chr2 243199373 2761937 0.011356678127620009 0.14807851818624537 chr3 198022430 2152463 0.010869793891530368 0.11300107209589115 chr4 191154276 2051005 0.01072957949420917 0.12570799477767397 chr5 180915260 1920754 0.010616871125188665 0.11180022481084623 chr6 171115067 1828982 0.010688608736015046 0.11499195808302629 chr7 159138663 1748913 0.010989868627965034 0.14644334822065974 chr8 146364022 1620923 0.011074600013383071 0.14926148662342514 chr9 141213431 1365806 0.009671927027960959 0.11501163752427156 chr10 135534747 1616769 0.0119288155678632 0.1450524161919957 chr11 135006516 1452584 0.010759362162934417 0.12027019704214237 chr12 133851895 1434274 0.010715380607797895 0.11229955074625252 chr13 115169878 986212 0.008563107099931112 0.100758711042983 chr14 107349540 959348 0.008936675462233 0.10327042826606472 chr15 102531392 956597 0.009329796283269031 0.1043926100841511 chr16 90354753 961670 0.010643269646257569 0.11358301793243884 chr17 81195210 936076 0.01152870963693548 0.11993591207238048 chr18 78077248 847279 0.010851804100472394 0.1552457386916921 chr19 59128983 737241 0.012468352449085755 0.1464773739209411 chr20 63025520 713567 0.011321874059904622 0.1175610157542773 chr21 48129895 444139 0.009227923725991922 0.11329581174452599 chr22 51304566 422004 0.008225466715769509 0.09843105963507046 chrMT 16571 11832 0.7140184659948102 1.0440116777223571 chrX 155270560 1798110 0.011580495362417705 0.11912904311756675 chrY 59373566 122381 0.0020612034655287507 0.08196869448642512