BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472648.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 = 8,606,592 number of mapped reads = 8,526,759 (99.07%) number of supplementary alignments = 39,059 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,268,212 number of mapped paired reads (second in pair) = 4,258,547 number of mapped paired reads (both in pair) = 8,480,708 number of mapped paired reads (singletons) = 46,051 number of mapped bases = 837,292,998 bp number of sequenced bases = 837,188,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,574,947 duplication rate = 41.54% >>>>>>> Insert size mean insert size = 17,749.7599 std insert size = 1,283,892.5944 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 54.5508 >>>>>>> ACTG content number of A's = 224,009,906 bp (26.76%) number of C's = 196,181,852 bp (23.43%) number of T's = 223,769,045 bp (26.73%) number of G's = 193,118,881 bp (23.07%) number of N's = 108,568 bp (0.01%) GC percentage = 46.5% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 6,335,217 number of insertions = 46,871 mapped reads with insertion percentage = 0.54% number of deletions = 40,021 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.2705X std coverageData = 18.1951X There is a 2.15% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 117849031 0.4728133897006419 22.604086798073247 chr2 243199373 38137346 0.15681514935484642 7.100261139213531 chr3 198022430 51679430 0.2609776579350127 10.827061215922964 chr4 191154276 56617790 0.29618897983741677 33.65581901107206 chr5 180915260 56506918 0.31233914706808036 23.167195668333953 chr6 171115067 47097778 0.27524039130931705 13.56474266497214 chr7 159138663 83636226 0.5255556658786307 32.034205856062854 chr8 146364022 41539873 0.2838120491113588 14.257039058675613 chr9 141213431 24059278 0.17037528108781663 9.519728842041454 chr10 135534747 18409757 0.13583053355314118 7.6841977613727055 chr11 135006516 33402380 0.2474130952316405 22.840445458079316 chr12 133851895 27044169 0.20204546973354393 7.811773783622975 chr13 115169878 26430834 0.2294943301060022 18.25546846453267 chr14 107349540 23877529 0.2224278650844708 10.217442652803198 chr15 102531392 16928379 0.16510435165066326 9.406936292623135 chr16 90354753 49654902 0.5495549525767615 28.563830454202147 chr17 81195210 28945337 0.3564906969265798 14.310172003917845 chr18 78077248 11259413 0.14420863040664547 4.498609439765653 chr19 59128983 24674407 0.4172980110278575 13.287020314307888 chr20 63025520 21515398 0.3413759696072321 27.4509524495317 chr21 48129895 5251652 0.10911413789703883 8.23525789490622 chr22 51304566 10901250 0.21248108794059384 8.779866960391729 chrMT 16571 2362 0.14253816909057992 0.4250133448339594 chrX 155270560 19914271 0.12825529192398094 6.866715947167842 chrY 59373566 1957288 0.032965646698734585 4.787697290288403