BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472565.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,286,270 number of mapped reads = 16,081,112 (98.74%) number of supplementary alignments = 58,094 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,064,209 number of mapped paired reads (second in pair) = 8,016,903 number of mapped paired reads (both in pair) = 15,981,778 number of mapped paired reads (singletons) = 99,334 number of mapped bases = 1,576,218,279 bp number of sequenced bases = 1,576,030,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,171,043 duplication rate = 44.86% >>>>>>> Insert size mean insert size = 28,437.6877 std insert size = 1,679,480.2852 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 55.0151 >>>>>>> ACTG content number of A's = 429,898,894 bp (27.28%) number of C's = 360,859,220 bp (22.9%) number of T's = 425,814,393 bp (27.02%) number of G's = 359,214,660 bp (22.79%) number of N's = 243,553 bp (0.02%) GC percentage = 45.69% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 9,154,966 number of insertions = 81,590 mapped reads with insertion percentage = 0.5% number of deletions = 76,642 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.5092X std coverageData = 19.3848X There is a 5.14% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199092702 0.7987651192251192 27.234767883675502 chr2 243199373 143397606 0.5896298342841534 28.64365442406863 chr3 198022430 159789652 0.8069270334678753 17.949619376827766 chr4 191154276 69705286 0.36465459972237296 17.426001577814002 chr5 180915260 90743536 0.5015803310345407 18.570557114441446 chr6 171115067 94379734 0.551557122669975 16.03120919291549 chr7 159138663 56131459 0.3527204385272484 12.575657690225288 chr8 146364022 75259397 0.5141932831006789 23.672986012758717 chr9 141213431 76851953 0.5442255205880523 15.019083511913772 chr10 135534747 39889662 0.29431317712202615 10.808387757927726 chr11 135006516 61023622 0.4520050128543425 20.6178867325115 chr12 133851895 97832972 0.7309046465124756 25.649827600836197 chr13 115169878 36393157 0.3159954463093206 11.50925975390205 chr14 107349540 33794399 0.31480711514925913 9.962995019610993 chr15 102531392 36527558 0.3562573109316608 11.161798005671196 chr16 90354753 59245247 0.655695965435266 23.05871720755027 chr17 81195210 48668666 0.5994031667631625 16.31005941808907 chr18 78077248 31906350 0.4086510579881094 19.512418271909706 chr19 59128983 34880574 0.5899065438010324 19.28495247322974 chr20 63025520 27942835 0.4433574685302081 14.390344753213155 chr21 48129895 7705055 0.16008875564760738 6.807934058979061 chr22 51304566 22230885 0.43331201749177645 12.664334032978244 chrMT 16571 3820 0.2305232031862893 0.678621772223368 chrX 155270560 70303249 0.4527790007326566 20.700162196380195 chrY 59373566 2518903 0.042424654096066924 1.4806843674802068