BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514714.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 118,573,124 number of mapped reads = 117,841,307 (99.38%) number of supplementary alignments = 5,087,399 (4.29%) number of secondary alignments = 0 number of mapped bases = 11,361,117,709 bp number of sequenced bases = 11,354,688,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,312,981 duplication rate = 45.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9369 >>>>>>> ACTG content number of A's = 3,318,568,166 bp (29.23%) number of C's = 2,363,420,784 bp (20.81%) number of T's = 3,272,214,868 bp (28.82%) number of G's = 2,397,112,618 bp (21.11%) number of N's = 3,372,510 bp (0.03%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 63,305,800 number of insertions = 3,361,753 mapped reads with insertion percentage = 2.77% number of deletions = 3,239,577 mapped reads with deletion percentage = 2.66% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 3.67X std coverageData = 79.8582X There is a 11.28% of reference with a coverageData >= 1X There is a 7.58% of reference with a coverageData >= 2X There is a 6.16% of reference with a coverageData >= 3X There is a 5.47% of reference with a coverageData >= 4X There is a 5.01% of reference with a coverageData >= 5X There is a 4.68% of reference with a coverageData >= 6X There is a 4.43% of reference with a coverageData >= 7X There is a 4.21% of reference with a coverageData >= 8X There is a 4.03% of reference with a coverageData >= 9X There is a 3.87% of reference with a coverageData >= 10X There is a 3.73% of reference with a coverageData >= 11X There is a 3.6% of reference with a coverageData >= 12X There is a 3.48% of reference with a coverageData >= 13X There is a 3.37% of reference with a coverageData >= 14X There is a 3.27% of reference with a coverageData >= 15X There is a 3.18% of reference with a coverageData >= 16X There is a 3.09% of reference with a coverageData >= 17X There is a 3.01% of reference with a coverageData >= 18X There is a 2.93% of reference with a coverageData >= 19X There is a 2.86% of reference with a coverageData >= 20X There is a 2.79% of reference with a coverageData >= 21X There is a 2.72% of reference with a coverageData >= 22X There is a 2.66% of reference with a coverageData >= 23X There is a 2.6% of reference with a coverageData >= 24X There is a 2.54% of reference with a coverageData >= 25X There is a 2.49% of reference with a coverageData >= 26X There is a 2.44% of reference with a coverageData >= 27X There is a 2.39% of reference with a coverageData >= 28X There is a 2.34% of reference with a coverageData >= 29X There is a 2.29% of reference with a coverageData >= 30X There is a 2.25% of reference with a coverageData >= 31X There is a 2.2% of reference with a coverageData >= 32X There is a 2.16% of reference with a coverageData >= 33X There is a 2.12% of reference with a coverageData >= 34X There is a 2.08% of reference with a coverageData >= 35X There is a 2.05% of reference with a coverageData >= 36X There is a 2.01% of reference with a coverageData >= 37X There is a 1.98% of reference with a coverageData >= 38X There is a 1.94% of reference with a coverageData >= 39X There is a 1.91% of reference with a coverageData >= 40X There is a 1.88% of reference with a coverageData >= 41X There is a 1.85% of reference with a coverageData >= 42X There is a 1.82% of reference with a coverageData >= 43X There is a 1.79% of reference with a coverageData >= 44X There is a 1.76% of reference with a coverageData >= 45X There is a 1.73% of reference with a coverageData >= 46X There is a 1.7% of reference with a coverageData >= 47X There is a 1.68% of reference with a coverageData >= 48X There is a 1.65% of reference with a coverageData >= 49X There is a 1.63% of reference with a coverageData >= 50X There is a 1.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1066958006 4.280663380975087 34.766593071345866 chr2 243199373 740379992 3.044333473672237 60.44195775804451 chr3 198022430 861835367 4.352210842983797 44.663194752739706 chr4 191154276 738705953 3.864449011854697 32.84206244382893 chr5 180915260 484515518 2.6781351556524307 31.43837438715141 chr6 171115067 545853559 3.1899795182852015 28.279570091415707 chr7 159138663 811735152 5.100804145878742 39.23201713352836 chr8 146364022 644885840 4.40604071402192 43.820427697974694 chr9 141213431 664128245 4.703010473557575 157.94809500827446 chr10 135534747 439947142 3.246009984435947 54.771287247209095 chr11 135006516 602902013 4.465725291362974 43.556645526450225 chr12 133851895 532430186 3.9777560564234076 37.460593556937496 chr13 115169878 426508885 3.7033023947459593 44.94507511226643 chr14 107349540 711125252 6.624390304793109 210.84412197046703 chr15 102531392 277437914 2.7058826432396432 29.860659547938734 chr16 90354753 98868577 1.0942266313317242 15.949581542798894 chr17 81195210 459596294 5.660386788826583 216.19379051378098 chr18 78077248 253639688 3.248573617758659 33.63744130441834 chr19 59128983 184431605 3.1191404898677186 37.221166384399204 chr20 63025520 231119783 3.6670825246661987 43.679448531080496 chr21 48129895 115526079 2.400297756726874 23.278768195834573 chr22 51304566 150148272 2.9266064154991587 93.57354231935767 chrMT 16571 6563181 396.0642689035061 211.55478007070184 chrX 155270560 271632803 1.7494160064857112 139.85025602000164 chrY 59373566 40242403 0.6777831569018442 13.957200164770276