BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777245.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 11,074,390 number of mapped reads = 10,668,342 (96.33%) number of supplementary alignments = 430,182 (3.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,357,842 number of mapped paired reads (second in pair) = 5,310,500 number of mapped paired reads (both in pair) = 10,575,200 number of mapped paired reads (singletons) = 93,142 number of mapped bases = 913,734,931 bp number of sequenced bases = 913,271,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,945,496 duplication rate = 15.4% >>>>>>> Insert size mean insert size = 247,486.819 std insert size = 4,856,583.6836 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 51.4925 >>>>>>> ACTG content number of A's = 256,384,820 bp (28.07%) number of C's = 175,669,971 bp (19.24%) number of T's = 277,534,587 bp (30.39%) number of G's = 203,665,003 bp (22.3%) number of N's = 17,111 bp (0%) GC percentage = 41.54% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 5,974,119 number of insertions = 93,289 mapped reads with insertion percentage = 0.86% number of deletions = 257,111 mapped reads with deletion percentage = 2.37% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.2952X std coverageData = 2.4915X There is a 13.86% of reference with a coverageData >= 1X There is a 7.55% of reference with a coverageData >= 2X There is a 3.37% of reference with a coverageData >= 3X There is a 1.79% of reference with a coverageData >= 4X There is a 0.92% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 75053596 0.3011169869863634 3.621139885173991 chr2 243199373 87237861 0.3587092348301408 2.7943948823516687 chr3 198022430 57351752 0.2896225038749398 0.928533472054203 chr4 191154276 57967147 0.30324797442668766 1.2123197161050168 chr5 180915260 61637774 0.3406996955370155 1.0197016034080526 chr6 171115067 44218832 0.2584157711839601 4.8627328027670895 chr7 159138663 63421381 0.3985290551297393 3.1853250913734654 chr8 146364022 46256153 0.3160349952668013 3.9011756765285392 chr9 141213431 34816016 0.24654889944569083 3.10020364021787 chr10 135534747 42611826 0.31439779793147804 2.2253735544205657 chr11 135006516 49121037 0.36384197189415657 2.041057554433521 chr12 133851895 41920705 0.3131872357877339 1.2723236990142366 chr13 115169878 40295051 0.34987491260518655 1.0269480924973489 chr14 107349540 19117263 0.17808425634613806 0.8505636569920713 chr15 102531392 33710071 0.3287780487755399 1.0034291909189161 chr16 90354753 24999613 0.27668287688197213 1.3909681402598542 chr17 81195210 23462556 0.28896478006522797 1.2354419050859444 chr18 78077248 20757886 0.2658634433426752 3.782796956424582 chr19 59128983 14338549 0.24249612072644644 2.462039219051139 chr20 63025520 24035132 0.38135555248096326 1.1096774812163492 chr21 48129895 8646130 0.17964157204165934 0.915594244502654 chr22 51304566 7863515 0.1532712507498845 0.6730775984066735 chrMT 16571 1846507 111.43002836280249 56.17441819103922 chrX 155270560 31287591 0.2015036913629989 1.0214629291405846 chrY 59373566 1760987 0.02965944474347389 1.0266288859901995