BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081913.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,788,401 number of mapped reads = 2,541,285 (91.14%) number of supplementary alignments = 17,593 (0.63%) number of secondary alignments = 0 number of mapped bases = 171,037,218 bp number of sequenced bases = 170,975,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,083 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3823 >>>>>>> ACTG content number of A's = 47,114,815 bp (27.56%) number of C's = 32,834,806 bp (19.2%) number of T's = 52,629,238 bp (30.78%) number of G's = 38,394,953 bp (22.46%) number of N's = 1,920 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,389,566 number of insertions = 12,009 mapped reads with insertion percentage = 0.47% number of deletions = 34,475 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.4699X There is a 4.63% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13416559 0.053827585047421 0.9234075479034994 chr2 243199373 14352948 0.0590172080747922 0.5240348612547726 chr3 198022430 11483862 0.057992733449438026 0.28341573848022084 chr4 191154276 11612122 0.06074738291493934 0.308184142150667 chr5 180915260 10567558 0.05841164531947167 0.2786084258739166 chr6 171115067 9502454 0.05553253823054635 0.3306167972020034 chr7 159138663 9469283 0.05950334646207251 0.5964747655857281 chr8 146364022 8401544 0.05740170217514247 0.5045283973417908 chr9 141213431 6809883 0.04822404605408957 0.3966809731473592 chr10 135534747 8302037 0.061253938076853455 0.5724951058366764 chr11 135006516 7806744 0.05782494231611754 0.41025142905316936 chr12 133851895 7385189 0.05517433279521369 0.2732902378705344 chr13 115169878 6180232 0.05366187849916799 0.2656508509474698 chr14 107349540 5188038 0.04832846046662147 0.27028540075809654 chr15 102531392 4949179 0.048269889869436276 0.25536578002546273 chr16 90354753 4590865 0.05080933595159073 0.3120479577738368 chr17 81195210 4264547 0.052522150013529126 0.30517175412457315 chr18 78077248 4855501 0.062188423956746015 0.7905746426211994 chr19 59128983 3201468 0.05414380287920731 0.6395920924544237 chr20 63025520 3062762 0.04859558477264448 0.26511279267202875 chr21 48129895 2560651 0.053202920970428044 0.2925846713444654 chr22 51304566 1841058 0.03588487621160269 0.21638132941527483 chrMT 16571 16820 1.015026250678897 1.1525744646404978 chrX 155270560 10724892 0.06907228260141524 0.3480917706979034 chrY 59373566 491022 0.008270043945145555 0.19031289891064587