BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818887.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,586,960 number of mapped reads = 1,420,928 (89.54%) number of supplementary alignments = 20,626 (1.3%) number of secondary alignments = 0 number of mapped bases = 131,641,300 bp number of sequenced bases = 131,555,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 218,655 duplication rate = 12.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1504 >>>>>>> ACTG content number of A's = 38,228,088 bp (29.06%) number of C's = 26,830,838 bp (20.4%) number of T's = 37,413,028 bp (28.44%) number of G's = 29,081,396 bp (22.11%) number of N's = 1,875 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 787,626 number of insertions = 16,784 mapped reads with insertion percentage = 1.14% number of deletions = 43,094 mapped reads with deletion percentage = 2.96% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.5521X There is a 3.26% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.16% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 11850537 0.047544663890727076 0.880116779444887 chr2 243199373 9643266 0.03965168939806436 0.7926901093413538 chr3 198022430 7735240 0.03906244358277999 0.24365346287798137 chr4 191154276 7619399 0.03985994537731398 0.32852894088477713 chr5 180915260 6851592 0.03787183015960069 0.2537805561804745 chr6 171115067 6270934 0.03664746833778232 0.2620553717760252 chr7 159138663 11153918 0.07008930318837729 1.170936953275108 chr8 146364022 12715372 0.08687498352566453 0.4622118681289459 chr9 141213431 4605556 0.03261414985377701 0.4439059603702436 chr10 135534747 5867482 0.0432913487491145 0.7263824767443862 chr11 135006516 5558075 0.04116893883847799 0.32024741878346097 chr12 133851895 4933621 0.036858805771857024 0.24010759305870305 chr13 115169878 3197794 0.02776588857721982 0.2023258696569044 chr14 107349540 4258973 0.039673882161022765 0.2747257389256972 chr15 102531392 3379127 0.03295699915982805 0.2211717583599263 chr16 90354753 3027299 0.033504590511137806 0.5350910683993845 chr17 81195210 3372824 0.0415396918118692 0.33529335028697793 chr18 78077248 2199822 0.028174942846346224 0.5080094341143475 chr19 59128983 2496756 0.04222558673129893 0.8428371653143973 chr20 63025520 5149037 0.0816976519987459 0.3778012994563729 chr21 48129895 1555281 0.03231424045284121 0.2667311070577651 chr22 51304566 1518425 0.029596293632032672 0.23223273589772056 chrMT 16571 221550 13.369742320922093 8.466887870296508 chrX 155270560 5937573 0.03824017250919943 0.2860168389375603 chrY 59373566 521847 0.008789214378668109 0.6320102999516745