BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124827.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 27,380,426 number of mapped reads = 27,003,211 (98.62%) number of supplementary alignments = 124,384 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,531,503 number of mapped paired reads (second in pair) = 13,471,708 number of mapped paired reads (both in pair) = 26,885,468 number of mapped paired reads (singletons) = 117,743 number of mapped bases = 2,342,119,504 bp number of sequenced bases = 2,340,716,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,258,661 duplication rate = 12.5% >>>>>>> Insert size mean insert size = 37,881.7921 std insert size = 1,823,513.7516 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7156 >>>>>>> ACTG content number of A's = 652,683,941 bp (27.88%) number of C's = 440,033,312 bp (18.8%) number of T's = 693,636,975 bp (29.63%) number of G's = 554,342,482 bp (23.68%) number of N's = 19,729 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 17,506,244 number of insertions = 323,250 mapped reads with insertion percentage = 1.16% number of deletions = 814,203 mapped reads with deletion percentage = 2.95% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.7566X std coverageData = 5.9418X There is a 28.17% of reference with a coverageData >= 1X There is a 15.53% of reference with a coverageData >= 2X There is a 9.17% of reference with a coverageData >= 3X There is a 5.83% of reference with a coverageData >= 4X There is a 3.87% of reference with a coverageData >= 5X There is a 2.65% of reference with a coverageData >= 6X There is a 1.87% of reference with a coverageData >= 7X There is a 1.35% of reference with a coverageData >= 8X There is a 0.99% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 176064179 0.7063740836176292 6.545797987005124 chr2 243199373 217171702 0.8929780505642998 9.634876870184774 chr3 198022430 171435026 0.8657353916927492 1.952835515717557 chr4 191154276 127727495 0.6681906242055501 4.413546368648472 chr5 180915260 122503452 0.6771316692688057 1.9269229910114118 chr6 171115067 136193784 0.7959192979774248 5.0046896787075354 chr7 159138663 131745788 0.8278678827407265 7.657214419774883 chr8 146364022 171873459 1.1742876196719985 4.4962948733796 chr9 141213431 95994790 0.6797851261046125 8.40101674141323 chr10 135534747 113880619 0.8402319074679794 10.085124936977357 chr11 135006516 92144025 0.6825153905904808 5.290551294771058 chr12 133851895 142119653 1.0617679562922886 2.4226397906859622 chr13 115169878 46949684 0.40765593239579534 1.2685865917864112 chr14 107349540 60567599 0.5642092085350342 1.956938855178329 chr15 102531392 43256241 0.42188290001953743 1.3230292452298313 chr16 90354753 64362945 0.7123360184494113 6.0924285554225195 chr17 81195210 82887948 1.020847756905857 10.419574563578841 chr18 78077248 49644502 0.6358382662257768 8.108598934228883 chr19 59128983 44843529 0.7584018314673195 3.5064581680782774 chr20 63025520 48418985 0.7682441176209256 2.3928476882132577 chr21 48129895 29880056 0.620821134141265 2.8032499969615072 chr22 51304566 28565121 0.5567754144923476 1.9451737105079323 chrMT 16571 3780941 228.16613360690363 137.28088986646992 chrX 155270560 132853537 0.8556260568648687 3.064208440128669 chrY 59373566 7254444 0.12218306038751318 7.692466563169971