BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708504.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,300,309 number of mapped reads = 2,156,623 (65.35%) number of supplementary alignments = 1,082 (0.03%) number of secondary alignments = 0 number of mapped bases = 101,993,932 bp number of sequenced bases = 101,968,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,115 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.9216 >>>>>>> ACTG content number of A's = 28,583,376 bp (28.03%) number of C's = 19,241,351 bp (18.87%) number of T's = 32,259,416 bp (31.64%) number of G's = 21,882,979 bp (21.46%) number of N's = 1,369 bp (0%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 538,741 number of insertions = 5,968 mapped reads with insertion percentage = 0.28% number of deletions = 16,572 mapped reads with deletion percentage = 0.77% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3109X There is a 2.89% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% 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 8501301 0.03410744160192082 0.42015798142101873 chr2 243199373 8830709 0.036310574698726714 0.5390085281580604 chr3 198022430 6952743 0.035110886175874115 0.22195487249713558 chr4 191154276 6493268 0.033968730053415074 0.22224981488090176 chr5 180915260 6269916 0.034656645326657354 0.2160550305527968 chr6 171115067 6103643 0.035669816264630866 0.34555219547855914 chr7 159138663 5650799 0.03550864945999955 0.37738465350438255 chr8 146364022 5224917 0.03569809662650566 0.369432020900079 chr9 141213431 4233663 0.029980597242198585 0.2644593414281141 chr10 135534747 4803074 0.03543795304387885 0.2632673459178735 chr11 135006516 4854279 0.03595588675142169 0.2705267523590405 chr12 133851895 4864185 0.03634005331041447 0.22281912809380258 chr13 115169878 3267537 0.02837145490420681 0.2617528577111702 chr14 107349540 3272788 0.030487210285204763 0.20962092014537842 chr15 102531392 3080576 0.030045198254989067 0.20930792619486682 chr16 90354753 2988703 0.033077429806044625 0.22449365314890035 chr17 81195210 2990946 0.0368364833344233 0.24112883981798477 chr18 78077248 2618401 0.03353603088059661 0.3464025339240824 chr19 59128983 2189432 0.03702806794427701 0.33905183083911117 chr20 63025520 2113275 0.03353046511952618 0.21960080046218958 chr21 48129895 1281105 0.02661765624047175 0.196979117734976 chr22 51304566 1240521 0.024179543785634985 0.1818539927010807 chrMT 16571 97815 5.902781968499185 4.189604704261622 chrX 155270560 3367002 0.021684741782344315 0.20969033539872542 chrY 59373566 703334 0.011845911360621325 0.142076043586216