BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524897.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,832,298 number of mapped reads = 1,675,139 (91.42%) number of supplementary alignments = 6,200 (0.34%) number of secondary alignments = 0 number of mapped bases = 97,238,185 bp number of sequenced bases = 97,208,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,201 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1176 >>>>>>> ACTG content number of A's = 25,117,126 bp (25.84%) number of C's = 17,713,616 bp (18.22%) number of T's = 31,660,220 bp (32.57%) number of G's = 22,704,497 bp (23.36%) number of N's = 12,661 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 485,591 number of insertions = 6,814 mapped reads with insertion percentage = 0.4% number of deletions = 18,944 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.314X There is a 2.81% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 7802837 0.0313051857953044 0.6126020620376306 chr2 243199373 8233964 0.03385684715560513 0.32897397169297365 chr3 198022430 6469899 0.032672556336168584 0.19645520981372547 chr4 191154276 6386661 0.03341102869181958 0.2238276080471993 chr5 180915260 5977288 0.03303915877521885 0.1992875827491954 chr6 171115067 5631600 0.03291118718376798 0.21924048824162545 chr7 159138663 5410781 0.034000417610646885 0.428611589368653 chr8 146364022 5021099 0.034305554953935335 0.3271526250706531 chr9 141213431 4082774 0.028912079899821995 0.28482052516103407 chr10 135534747 4669717 0.03445402085710168 0.2935730563470268 chr11 135006516 4450635 0.032966075504089004 0.27879539822026395 chr12 133851895 4329120 0.03234261270637969 0.20194072804601917 chr13 115169878 3024413 0.026260451539247092 0.17754425979100455 chr14 107349540 2962943 0.02760089144303739 0.1910943681622379 chr15 102531392 2773789 0.027053070731742332 0.1805108872673225 chr16 90354753 2744178 0.030371152694092362 0.20801413137779887 chr17 81195210 2537820 0.031255784670056276 0.2097523135550281 chr18 78077248 2654233 0.03399496099042835 0.5572852785840522 chr19 59128983 1866708 0.03157010158622211 0.4185847583965297 chr20 63025520 2031378 0.03223103910923702 0.19757638564426092 chr21 48129895 1256360 0.026103526716607216 0.19864995936886656 chr22 51304566 1107068 0.021578352304939097 0.15832254470683912 chrMT 16571 29078 1.754752278076157 1.8147131873843663 chrX 155270560 5484359 0.03532130624118313 0.23927890037297075 chrY 59373566 299483 0.005044046032202276 0.13559802185424372