BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708595.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 = 4,756,831 number of mapped reads = 4,682,432 (98.44%) number of supplementary alignments = 126 (0%) number of secondary alignments = 0 number of mapped bases = 233,597,088 bp number of sequenced bases = 233,577,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,223 duplication rate = 0.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8232 >>>>>>> ACTG content number of A's = 72,397,670 bp (31%) number of C's = 44,262,116 bp (18.95%) number of T's = 72,124,353 bp (30.88%) number of G's = 44,785,002 bp (19.17%) number of N's = 8,399 bp (0%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 333,186 number of insertions = 14,517 mapped reads with insertion percentage = 0.31% number of deletions = 11,553 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.6% >>>>>>> Coverage mean coverageData = 0.0755X std coverageData = 0.2859X There is a 7% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.04% 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 17719136 0.0710896363223103 0.2793321850462518 chr2 243199373 20855626 0.08575526220620643 0.3044048980876101 chr3 198022430 18492266 0.0933847039449016 0.3166254271610708 chr4 191154276 18375818 0.09613082367040536 0.3206292566624105 chr5 180915260 16286107 0.09002063728620792 0.31021041345307127 chr6 171115067 15648447 0.09144984877339878 0.3132673280182374 chr7 159138663 12769742 0.08024286342031163 0.29449699214272645 chr8 146364022 12890401 0.08807083068542623 0.3072409094511961 chr9 141213431 9641301 0.0682746742411492 0.27193379414250857 chr10 135534747 9898467 0.07303268880562414 0.27995737271891197 chr11 135006516 10907780 0.08079447069058504 0.29614258145798295 chr12 133851895 10425644 0.07788940156581273 0.2898719855310302 chr13 115169878 8890005 0.07719036569614149 0.2891844702489531 chr14 107349540 7248862 0.06752578539228021 0.2709104833621022 chr15 102531392 6207966 0.06054697862679949 0.257179378306986 chr16 90354753 4397918 0.048673897653176035 0.22929369358660928 chr17 81195210 3852051 0.047441850325899766 0.2260700993462751 chr18 78077248 6538830 0.08374821305177149 0.2994075875747143 chr19 59128983 1773396 0.02999199225192153 0.17849283608772173 chr20 63025520 3580026 0.056802799881698715 0.24780799689642494 chr21 48129895 3070756 0.06380142736650475 0.2650421188695502 chr22 51304566 1196463 0.02332078981040401 0.15795760428952182 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 12630132 0.0813427349009368 0.2950747797045648 chrY 59373566 299848 0.005050193549095569 0.07436788065526075