BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472633.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 = 19,266,132 number of mapped reads = 19,121,657 (99.25%) number of supplementary alignments = 86,829 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,586,877 number of mapped paired reads (second in pair) = 9,534,780 number of mapped paired reads (both in pair) = 19,021,256 number of mapped paired reads (singletons) = 100,401 number of mapped bases = 1,884,224,440 bp number of sequenced bases = 1,883,989,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,212,232 duplication rate = 51.13% >>>>>>> Insert size mean insert size = 19,167.8989 std insert size = 1,374,414.0909 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.875 >>>>>>> ACTG content number of A's = 506,051,605 bp (26.86%) number of C's = 437,742,461 bp (23.23%) number of T's = 507,357,811 bp (26.93%) number of G's = 432,488,027 bp (22.96%) number of N's = 349,247 bp (0.02%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,573,910 number of insertions = 111,267 mapped reads with insertion percentage = 0.58% number of deletions = 97,808 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.6087X std coverageData = 23.7736X There is a 3.65% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 257807079 1.034328732926206 31.52937575434996 chr2 243199373 131821430 0.5420303036718767 30.164068811481773 chr3 198022430 124891790 0.6306951692290615 17.84265330951607 chr4 191154276 55419997 0.2899228736060291 13.508948086323416 chr5 180915260 90854867 0.5021957075373299 22.494213804162175 chr6 171115067 157623721 0.9211562942028945 30.634332414780054 chr7 159138663 84161495 0.5288563659731137 18.34027957573459 chr8 146364022 148641649 1.015561385707206 37.762311316842556 chr9 141213431 97607764 0.6912073682283096 19.57245307741677 chr10 135534747 38050883 0.280746331418614 11.236034139960553 chr11 135006516 64836820 0.48024956069527786 20.56296923061316 chr12 133851895 57948010 0.4329263324960771 13.488411033902164 chr13 115169878 56138549 0.4874412474414534 20.293164684951467 chr14 107349540 27937837 0.26025111053107447 15.078974687986006 chr15 102531392 31022688 0.3025677053131201 11.240211955776138 chr16 90354753 75786106 0.8387616974615603 28.719237357944973 chr17 81195210 70315240 0.8660023171317618 21.372224869828617 chr18 78077248 38532218 0.4935140388144828 28.9328396287902 chr19 59128983 43359101 0.7332969180274925 20.881351874639893 chr20 63025520 92013363 1.45993818059732 45.93860239150323 chr21 48129895 7943895 0.16505115999110323 6.656825867585067 chr22 51304566 27070943 0.5276517298674742 18.320835801322172 chrMT 16571 1133 0.06837245790839418 0.2656636090445707 chrX 155270560 103314166 0.6653815507588818 22.04043743741397 chrY 59373566 1123696 0.018925863405273653 0.9461592401014636