BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695912.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,134,411 number of mapped reads = 13,983,678 (92.4%) number of supplementary alignments = 224,334 (1.48%) number of secondary alignments = 0 number of mapped bases = 2,060,900,308 bp number of sequenced bases = 2,047,717,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,022,315 duplication rate = 18.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.2071 >>>>>>> ACTG content number of A's = 583,714,828 bp (28.51%) number of C's = 436,011,654 bp (21.29%) number of T's = 580,830,664 bp (28.36%) number of G's = 447,160,655 bp (21.84%) number of N's = 0 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0172 number of mismatches = 20,736,193 number of insertions = 13,333,008 mapped reads with insertion percentage = 51.85% number of deletions = 11,859,381 mapped reads with deletion percentage = 49.81% homopolymer indels = 37.1% >>>>>>> Coverage mean coverageData = 0.6657X std coverageData = 1.5555X There is a 29.47% of reference with a coverageData >= 1X There is a 15.45% of reference with a coverageData >= 2X There is a 8.48% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 2.85% of reference with a coverageData >= 5X There is a 1.73% of reference with a coverageData >= 6X There is a 1.08% of reference with a coverageData >= 7X There is a 0.69% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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% 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 198560961 0.7966317604480512 2.1278749482228703 chr2 243199373 165687986 0.6812845936078955 1.49648288515616 chr3 198022430 142056372 0.7173751579555911 1.4684729377225239 chr4 191154276 106274192 0.5559603176232375 1.3195257757029124 chr5 180915260 123595517 0.6831680036277757 1.4569627967529062 chr6 171115067 121524912 0.7101941058176952 1.5052535272480532 chr7 159138663 103992806 0.6534729150011773 1.4443231273421915 chr8 146364022 102453433 0.6999905550559413 1.474205303828351 chr9 141213431 84138858 0.595827588099605 1.4608676335588748 chr10 135534747 101000382 0.7451991775953956 1.7596354221515076 chr11 135006516 105538995 0.7817326017064243 1.6226983762636884 chr12 133851895 102313092 0.7643753717494997 1.553422745730214 chr13 115169878 55394191 0.4809781165175846 1.217046970612742 chr14 107349540 64992839 0.6054319282597764 1.3921125118460773 chr15 102531392 69693125 0.6797247520057077 1.470364079688674 chr16 90354753 69611470 0.7704239975068052 1.6041364549948458 chr17 81195210 69263594 0.8530502476685509 1.856273251503612 chr18 78077248 51100273 0.6544835314892247 1.7562384854406337 chr19 59128983 47451630 0.8025105048737267 1.9155135985265264 chr20 63025520 56317065 0.8935597040690818 1.726660857151459 chr21 48129895 24772419 0.5146992113737211 1.4026328045052592 chr22 51304566 29114823 0.5674898994370209 1.3926769257356013 chrMT 16571 378398 22.834952628085208 14.284802623422625 chrX 155270560 56692046 0.3651178046887961 1.0206140763506797 chrY 59373566 8980929 0.15126140478070663 0.959745628766287