BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234049.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,100,630 number of mapped reads = 1,965,563 (93.57%) number of supplementary alignments = 14,560 (0.69%) number of secondary alignments = 0 number of mapped bases = 132,666,454 bp number of sequenced bases = 132,597,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,106 duplication rate = 5.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9746 >>>>>>> ACTG content number of A's = 36,235,945 bp (27.33%) number of C's = 25,111,995 bp (18.94%) number of T's = 41,224,456 bp (31.09%) number of G's = 30,012,965 bp (22.63%) number of N's = 11,795 bp (0.01%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,054,784 number of insertions = 12,031 mapped reads with insertion percentage = 0.61% number of deletions = 39,824 mapped reads with deletion percentage = 2% homopolymer indels = 44.14% >>>>>>> Coverage mean coverageData = 0.0429X std coverageData = 0.5862X There is a 3.69% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% 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 0.01% 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 11562723 0.04638994660719421 1.3173881744681264 chr2 243199373 9315180 0.03830264809111987 0.5833149952847273 chr3 198022430 14033506 0.07086826477182408 0.3127242222109232 chr4 191154276 4635970 0.024252504819719543 0.21176200800475453 chr5 180915260 7222439 0.03992166829929106 0.22858967102028557 chr6 171115067 9890406 0.057799737763595066 0.46085131619182174 chr7 159138663 7939773 0.04989216856748382 0.8453771589611627 chr8 146364022 6511533 0.04448861756477285 0.6188486128792725 chr9 141213431 5832359 0.04130173000328843 0.4327244246897187 chr10 135534747 7134774 0.05264165948529789 0.7292016195155093 chr11 135006516 5308841 0.039322850165246837 0.3818352369218511 chr12 133851895 4559683 0.03406513594745894 0.2185653844983761 chr13 115169878 5523315 0.04795798255512609 0.247930059648749 chr14 107349540 4920012 0.045831700815858176 0.28887085656257117 chr15 102531392 2167877 0.021143544018206638 0.1746928711689814 chr16 90354753 4190873 0.046382429931494586 0.31773046597728843 chr17 81195210 3274812 0.040332576268969564 0.273695452973131 chr18 78077248 2572382 0.03294662742211406 1.0253061329873783 chr19 59128983 3624865 0.06130436912808056 0.8172911373182054 chr20 63025520 2824549 0.044815957091667 0.2651932134573115 chr21 48129895 2504975 0.052046134736009705 0.2825363780014434 chr22 51304566 1021307 0.01990674670164835 0.15366813268440138 chrMT 16571 112984 6.818176332146521 5.1091008517632 chrX 155270560 5610919 0.036136399585343155 0.27770846091658635 chrY 59373566 370397 0.006238415930752752 0.15453082991061573