BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084887.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,551,038 number of mapped reads = 2,249,373 (88.17%) number of supplementary alignments = 14,419 (0.57%) number of secondary alignments = 0 number of mapped bases = 155,692,040 bp number of sequenced bases = 155,628,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,592 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5003 >>>>>>> ACTG content number of A's = 45,347,340 bp (29.14%) number of C's = 28,445,674 bp (18.28%) number of T's = 49,473,957 bp (31.79%) number of G's = 32,337,253 bp (20.78%) number of N's = 24,474 bp (0.02%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,358,081 number of insertions = 12,961 mapped reads with insertion percentage = 0.57% number of deletions = 35,797 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.0503X std coverageData = 0.4922X There is a 4.36% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% 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 12968663 0.05203061459975259 1.0808961722026256 chr2 243199373 14436000 0.059358705665741994 0.5020846644177543 chr3 198022430 11043117 0.0557670007382497 0.26320283125692073 chr4 191154276 10213874 0.053432621093969145 0.2725822743710527 chr5 180915260 9131573 0.05047431045894083 0.2638068278599802 chr6 171115067 9164211 0.053555839124324454 0.26344148024765174 chr7 159138663 8589118 0.053972540915465654 0.4351722343436158 chr8 146364022 8064013 0.055095595828871115 0.8385260983862414 chr9 141213431 9437279 0.0668298966548019 0.4705587923950642 chr10 135534747 6736995 0.0497067737175914 0.3782780060721353 chr11 135006516 5973081 0.04424290898670402 0.34987627640431085 chr12 133851895 6250631 0.046698113612810635 0.24440595027949266 chr13 115169878 5441630 0.047248725921199636 0.2386280748169841 chr14 107349540 3271676 0.030476851600854553 0.21537416845353805 chr15 102531392 3656821 0.03566537943813344 0.2096899902280025 chr16 90354753 3338183 0.03694529495310556 0.26910580483666924 chr17 81195210 4073399 0.05016797173133735 0.2629636799378211 chr18 78077248 4464022 0.05717442807410425 0.8995029450241452 chr19 59128983 2991329 0.05058989429938276 0.5624782833363664 chr20 63025520 2795463 0.044354461494328014 0.2532421497450644 chr21 48129895 2403387 0.049935429944320466 0.26679059826716156 chr22 51304566 1546964 0.03015255991055455 0.18926747603535501 chrMT 16571 124780 7.53002232816366 4.571953097487706 chrX 155270560 9211175 0.059323383647228424 0.30802080037364943 chrY 59373566 364656 0.006141723069151683 0.1441419476798989