BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237865.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,280,106 number of mapped reads = 2,046,086 (89.74%) number of supplementary alignments = 13,533 (0.59%) number of secondary alignments = 0 number of mapped bases = 131,950,363 bp number of sequenced bases = 131,896,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,471 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2824 >>>>>>> ACTG content number of A's = 35,907,845 bp (27.22%) number of C's = 23,957,868 bp (18.16%) number of T's = 41,368,156 bp (31.36%) number of G's = 30,559,446 bp (23.17%) number of N's = 102,816 bp (0.08%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 952,509 number of insertions = 10,923 mapped reads with insertion percentage = 0.53% number of deletions = 32,142 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.4348X There is a 3.7% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 13244574 0.053137576736468795 0.9428700527197137 chr2 243199373 8093826 0.033280620341073 0.3340943786315316 chr3 198022430 9795053 0.04946436118373055 0.2578522856527191 chr4 191154276 2504251 0.013100679997344135 0.21279587571628936 chr5 180915260 8178109 0.045204086156137406 0.23729014867830284 chr6 171115067 8475256 0.049529571817308174 0.2997088145371805 chr7 159138663 7352376 0.04620106680172373 0.5038912771980382 chr8 146364022 4967803 0.03394142175185648 0.26205197807217445 chr9 141213431 8916394 0.06314126026723337 0.45729867747793257 chr10 135534747 9328760 0.06882928700195234 0.6371647808397208 chr11 135006516 8394943 0.06218176165660034 0.4214236270228353 chr12 133851895 7446454 0.055632040173954955 0.2722962683062751 chr13 115169878 1894161 0.016446670196177512 0.1398234330409275 chr14 107349540 1706130 0.015893221340305696 0.1988335591173986 chr15 102531392 1957598 0.01909266968695792 0.15110653279584496 chr16 90354753 2484299 0.027494945395954987 0.25911219973575417 chr17 81195210 4838926 0.0595962003177281 0.4539053347383196 chr18 78077248 844300 0.01081364957945239 0.6413130669251094 chr19 59128983 1738483 0.029401537313773856 0.6072396801124322 chr20 63025520 2781018 0.04412526862134577 0.2450292719005043 chr21 48129895 1872167 0.03889821492442483 0.2915438283197277 chr22 51304566 1646109 0.03208503898074101 0.1968158830922606 chrMT 16571 68743 4.14839176875264 3.14062288985353 chrX 155270560 12993892 0.08368548422830445 0.36034314443123705 chrY 59373566 426738 0.0071873399013965234 0.22197301803478192