BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124903.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,884,712 number of mapped reads = 3,842,781 (98.92%) number of supplementary alignments = 16,676 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,922,663 number of mapped paired reads (second in pair) = 1,920,118 number of mapped paired reads (both in pair) = 3,830,248 number of mapped paired reads (singletons) = 12,533 number of mapped bases = 353,107,119 bp number of sequenced bases = 352,916,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,848 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 63,259.4187 std insert size = 2,467,740.7557 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.5574 >>>>>>> ACTG content number of A's = 102,351,984 bp (29%) number of C's = 71,920,015 bp (20.38%) number of T's = 103,474,240 bp (29.32%) number of G's = 74,939,720 bp (21.23%) number of N's = 230,766 bp (0.07%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,030,160 number of insertions = 51,337 mapped reads with insertion percentage = 1.31% number of deletions = 112,353 mapped reads with deletion percentage = 2.86% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 1.2673X There is a 7.91% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 26440618 0.10608044984569968 1.7613750891050683 chr2 243199373 35875661 0.14751543376717505 1.2431141582838616 chr3 198022430 28728933 0.14507918623157992 0.5105194103221732 chr4 191154276 15744557 0.08236570653538507 0.7238316238656531 chr5 180915260 29216605 0.16149331460485974 0.5186927137537046 chr6 171115067 21832901 0.1275919261978257 1.0935231901688875 chr7 159138663 28206882 0.1772471973074199 2.0843893961537083 chr8 146364022 15032996 0.10270963994143315 0.5481529507373081 chr9 141213431 14546228 0.10300881365880842 1.5308665397927705 chr10 135534747 19650426 0.14498441495596698 2.965447927914405 chr11 135006516 15590444 0.11547919657448237 0.7998034496371238 chr12 133851895 14817161 0.11069817875944155 0.4261149825605834 chr13 115169878 7272952 0.06314977602042784 0.3086745922186471 chr14 107349540 7180203 0.06688620184120025 0.371998016996651 chr15 102531392 8297500 0.0809264347059679 0.3572659838928452 chr16 90354753 14917895 0.16510360002865593 2.2998015632533493 chr17 81195210 7842931 0.09659351826296157 1.505888061746877 chr18 78077248 9671590 0.12387206577772823 1.5424349342384427 chr19 59128983 5699733 0.09639491009003148 0.9669672998626584 chr20 63025520 9381804 0.1488572248194065 0.5223097665441837 chr21 48129895 3179725 0.0660654879882867 0.4103288135178108 chr22 51304566 2734766 0.05330453433715822 0.3027220237070657 chrMT 16571 1201 0.07247601231066321 0.29325707840207343 chrX 155270560 10489281 0.06755486036760606 0.48730614652771514 chrY 59373566 754126 0.012701376231975018 0.7729594879058651