BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094006.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 485,424 number of mapped reads = 296,211 (61.02%) number of supplementary alignments = 2,434 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,752 number of mapped paired reads (second in pair) = 148,459 number of mapped paired reads (both in pair) = 292,410 number of mapped paired reads (singletons) = 3,801 number of mapped bases = 41,698,543 bp number of sequenced bases = 41,256,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 291,369 duplication rate = 40.42% >>>>>>> Insert size mean insert size = 49,303.734 std insert size = 2,193,860.0764 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 22.5732 >>>>>>> ACTG content number of A's = 11,679,746 bp (28.31%) number of C's = 8,630,004 bp (20.92%) number of T's = 11,757,578 bp (28.5%) number of G's = 9,189,005 bp (22.27%) number of N's = 531 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0286 number of mismatches = 1,172,096 number of insertions = 7,979 mapped reads with insertion percentage = 2.62% number of deletions = 71,166 mapped reads with deletion percentage = 23.09% homopolymer indels = 39.5% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 14.9499X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 166822 6.692942201335578E-4 0.5573055487485185 chr2 243199373 608264 0.0025010919744435363 1.4735399369259565 chr3 198022430 523309 0.0026426753777337242 2.5479717433050255 chr4 191154276 1531904 0.008013966687305493 6.005559943219199 chr5 180915260 64731 3.577973466693744E-4 0.23126757571956014 chr6 171115067 4333644 0.02532590540375968 25.092697950501982 chr7 159138663 693585 0.004358368902470922 3.5400854471301466 chr8 146364022 116010 7.926128184698286E-4 0.6646158899513258 chr9 141213431 63100 4.4684134896488706E-4 0.3125522479386476 chr10 135534747 1383434 0.010207227523728657 7.880671667804092 chr11 135006516 1216541 0.009010979884852372 6.939582999034944 chr12 133851895 465035 0.0034742504019087666 1.9399033476407677 chr13 115169878 734007 0.006373254992941817 3.595897454387612 chr14 107349540 16820 1.5668441616051637E-4 0.07173346086466255 chr15 102531392 7496 7.31093166081272E-5 0.022306039527040192 chr16 90354753 36018 3.986287251540602E-4 0.20864259174781502 chr17 81195210 849215 0.01045892978169525 6.653246823592249 chr18 78077248 167916 0.002150639325812303 1.4880439475734901 chr19 59128983 203653 0.003444216180751832 1.1066847083626754 chr20 63025520 219617 0.0034845725985283424 1.8208589025673276 chr21 48129895 96891 0.002013114717993879 0.9963779077274433 chr22 51304566 77195 0.0015046419065312823 0.8248659191601074 chrMT 16571 18505255 1116.725303240601 5188.566236732724 chrX 155270560 9611954 0.061904549065837075 23.4642330439086 chrY 59373566 6127 1.0319407124712704E-4 0.037719730864191926