BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053680.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,182,848 number of mapped reads = 5,933,742 (82.61%) number of supplementary alignments = 256 (0%) number of secondary alignments = 0 number of mapped bases = 279,384,229 bp number of sequenced bases = 279,325,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,200,061 duplication rate = 15.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4184 >>>>>>> ACTG content number of A's = 80,400,723 bp (28.78%) number of C's = 55,483,048 bp (19.86%) number of T's = 81,898,291 bp (29.32%) number of G's = 61,531,704 bp (22.03%) number of N's = 11,243 bp (0%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,330,729 number of insertions = 11,171 mapped reads with insertion percentage = 0.19% number of deletions = 38,725 mapped reads with deletion percentage = 0.65% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0902X std coverageData = 0.6845X There is a 4.25% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 23552119 0.094491716431872 0.7913569539210756 chr2 243199373 28898478 0.11882628496743698 0.8408427267120218 chr3 198022430 16618360 0.0839216042344294 0.6028075869531359 chr4 191154276 13548718 0.07087844584758334 0.5593061849371356 chr5 180915260 13148812 0.07267939697292533 0.5475539640652117 chr6 171115067 17445814 0.10195369879380639 0.7176530562587858 chr7 159138663 14544631 0.09139596076661773 0.7103639447557452 chr8 146364022 15160659 0.10358186932031699 0.7173372724251829 chr9 141213431 14695390 0.10406510128629337 0.7148599000174767 chr10 135534747 10023111 0.07395233489460824 0.6401822330051368 chr11 135006516 13590728 0.10066720038905382 0.7088568371860846 chr12 133851895 15096502 0.1127851197026385 0.7290655668819352 chr13 115169878 7639603 0.06633334282076778 0.5694114556064466 chr14 107349540 5407648 0.05037420747215125 0.5266298884077447 chr15 102531392 7344442 0.07163115468090007 0.5621777659588406 chr16 90354753 7494296 0.08294301905733725 0.6443744839611688 chr17 81195210 6747383 0.08310075187932885 0.6080234287965315 chr18 78077248 9078120 0.11627100381406885 0.8171195268780316 chr19 59128983 6248558 0.10567673724406862 0.7857390121908145 chr20 63025520 6578916 0.10438495390438667 0.7048273135517741 chr21 48129895 2919967 0.060668468111139656 0.6334102572407623 chr22 51304566 4341264 0.08461749778762381 0.6180026043743737 chrMT 16571 16602 1.0018707380363285 2.1246666859405514 chrX 155270560 18553023 0.11948834988422789 0.779644714555036 chrY 59373566 691085 0.011639607430687253 0.2680471910285301