BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536756.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 20,543,897 number of mapped reads = 19,814,361 (96.45%) number of supplementary alignments = 448 (0%) number of secondary alignments = 0 number of mapped bases = 988,134,785 bp number of sequenced bases = 988,049,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,426 duplication rate = 0.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6726 >>>>>>> ACTG content number of A's = 309,918,615 bp (31.37%) number of C's = 182,954,879 bp (18.52%) number of T's = 309,192,333 bp (31.29%) number of G's = 185,565,313 bp (18.78%) number of N's = 417,944 bp (0.04%) GC percentage = 37.3% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,472,447 number of insertions = 55,333 mapped reads with insertion percentage = 0.28% number of deletions = 51,701 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.3192X std coverageData = 0.6245X There is a 25.02% of reference with a coverageData >= 1X There is a 5.55% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.04% 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 77178085 0.30964049233000707 0.6256937309820689 chr2 243199373 89899284 0.3696526141948565 0.6594727402278784 chr3 198022430 76781241 0.3877401211569821 0.6723150354638134 chr4 191154276 83942720 0.4391359783131401 0.7137945671954785 chr5 180915260 70261204 0.3883652711219606 0.6721230652299705 chr6 171115067 66883434 0.3908681752729583 0.6775741651582057 chr7 159138663 56462291 0.3547993299403301 0.6554368230062579 chr8 146364022 55946239 0.3822403773517511 0.6703514178812175 chr9 141213431 40989966 0.2902695990723432 0.600363426229457 chr10 135534747 42478501 0.31341410184651763 0.6085890905908087 chr11 135006516 44567030 0.33011021482844577 0.6356798828156726 chr12 133851895 46133407 0.3446600961458185 0.6463470325333062 chr13 115169878 42255644 0.3668984002917846 0.672075888960433 chr14 107349540 32410760 0.3019180147395136 0.6171757318481503 chr15 102531392 25647373 0.25014166393059406 0.5595148564315293 chr16 90354753 17788253 0.1968712481566963 0.4917932196356706 chr17 81195210 14899407 0.18350105874472153 0.47698063837761423 chr18 78077248 29740622 0.3809127852457095 0.6707948387883009 chr19 59128983 6449733 0.10907904504293606 0.3566957612646679 chr20 63025520 14609840 0.2318083214545473 0.5338305053463381 chr21 48129895 13102204 0.27222590034738287 0.6025129766873366 chr22 51304566 4806265 0.0936810380580941 0.33778494781992324 chrMT 16571 1819 0.1097700802606964 0.3463063392765491 chrX 155270560 30463548 0.19619654878555212 0.46451453501987217 chrY 59373566 4435915 0.07471195178002278 0.3036266494029264