BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080974.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,313,100 number of mapped reads = 5,534,251 (87.66%) number of supplementary alignments = 60,039 (0.95%) number of secondary alignments = 0 number of mapped bases = 373,204,624 bp number of sequenced bases = 373,068,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,487 duplication rate = 6.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1314 >>>>>>> ACTG content number of A's = 105,308,387 bp (28.23%) number of C's = 65,821,223 bp (17.64%) number of T's = 121,421,920 bp (32.55%) number of G's = 79,778,448 bp (21.38%) number of N's = 738,163 bp (0.2%) GC percentage = 39.03% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,724,577 number of insertions = 29,563 mapped reads with insertion percentage = 0.53% number of deletions = 82,314 mapped reads with deletion percentage = 1.47% homopolymer indels = 49.4% >>>>>>> Coverage mean coverageData = 0.1206X std coverageData = 0.8829X There is a 7.78% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 31830951 0.12770660659657895 1.4135302552420304 chr2 243199373 25919335 0.10657648776092857 0.7448730302875025 chr3 198022430 33782755 0.17060064862349178 0.5922074503364084 chr4 191154276 24636001 0.12888019831688202 0.5379505873637133 chr5 180915260 21709783 0.11999973357692435 0.4950597788225418 chr6 171115067 31219581 0.1824478787715403 0.8639180976293317 chr7 159138663 18607101 0.11692382384788541 0.8712863327980251 chr8 146364022 28882971 0.197336549005192 2.0104556713385775 chr9 141213431 18933828 0.13407951259253803 0.9565284809619895 chr10 135534747 15542148 0.11467279309563326 0.6491035462854042 chr11 135006516 16902039 0.12519424617993993 0.7274914311918201 chr12 133851895 15685578 0.11718607345828014 0.5066379908720635 chr13 115169878 9912177 0.08606570721556205 0.4131670930999843 chr14 107349540 10525734 0.09805103962252656 0.5672990907565699 chr15 102531392 9350674 0.09119815714586221 0.42455928607098653 chr16 90354753 8247957 0.0912841519250238 0.5258680178567149 chr17 81195210 7456062 0.09182884064220044 0.46723265836636846 chr18 78077248 9484927 0.1214813180915393 1.680164371902419 chr19 59128983 6657011 0.11258456787596026 1.0476265154679412 chr20 63025520 5999410 0.09519017058486784 0.4724043338577354 chr21 48129895 6757114 0.14039328363379974 0.6618558530246691 chr22 51304566 3586415 0.06990440188111133 0.3635779349798929 chrMT 16571 72970 4.403475951964275 3.1354148503839716 chrX 155270560 10698078 0.06889959049545516 0.4285281068335133 chrY 59373566 804024 0.013541783897568153 0.2470095229215962