BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008764.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 = 1,457,509 number of mapped reads = 1,271,969 (87.27%) number of supplementary alignments = 9,585 (0.66%) number of secondary alignments = 0 number of mapped bases = 83,650,016 bp number of sequenced bases = 83,609,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,101 duplication rate = 5.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1811 >>>>>>> ACTG content number of A's = 22,386,563 bp (26.78%) number of C's = 16,111,051 bp (19.27%) number of T's = 25,817,237 bp (30.88%) number of G's = 19,181,951 bp (22.94%) number of N's = 112,428 bp (0.13%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 708,256 number of insertions = 6,286 mapped reads with insertion percentage = 0.49% number of deletions = 22,688 mapped reads with deletion percentage = 1.76% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2931X There is a 1.94% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 6691131 0.026844992293920903 0.40466597400280396 chr2 243199373 6207775 0.025525456432817367 0.38855860023382977 chr3 198022430 5262508 0.026575312705737427 0.22094967194207993 chr4 191154276 4961035 0.025953042243219294 0.22735234765032628 chr5 180915260 5189053 0.0286822294592507 0.2251978018533059 chr6 171115067 4855175 0.028373743382866454 0.24260527595126796 chr7 159138663 4354652 0.02736388453885653 0.29498319070929363 chr8 146364022 3796590 0.025939366438017124 0.44618292187159253 chr9 141213431 3467716 0.024556559354471034 0.25117660544564946 chr10 135534747 4462234 0.03292317356817732 0.37551452371469535 chr11 135006516 3987719 0.029537233595451053 0.266608513013034 chr12 133851895 4007931 0.029943027702372088 0.23145948418789675 chr13 115169878 2383834 0.020698415604816393 0.19042318667164612 chr14 107349540 2669408 0.02486650618158215 0.2234237052865298 chr15 102531392 2598196 0.025340492792685385 0.2104723099339089 chr16 90354753 2583101 0.02858843518724466 0.2596809680356162 chr17 81195210 2770706 0.0341240080541697 0.25661207254381685 chr18 78077248 2155868 0.027611987553659678 0.3701462481353202 chr19 59128983 2132904 0.036072056236786616 0.3545005443175021 chr20 63025520 1828623 0.02901400892844676 0.23281307512032917 chr21 48129895 1250852 0.025989086408769436 0.22504408746042684 chr22 51304566 1117079 0.021773481136162422 0.19548479078082223 chrMT 16571 43915 2.650111640818297 2.531402611520155 chrX 155270560 4601410 0.029634787174078588 0.23764034771696305 chrY 59373566 270601 0.004557600599566481 0.14670455661805115