BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777304.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 215,557,934 number of mapped reads = 210,317,445 (97.57%) number of supplementary alignments = 767,342 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 105,513,852 number of mapped paired reads (second in pair) = 104,803,593 number of mapped paired reads (both in pair) = 209,393,030 number of mapped paired reads (singletons) = 924,415 number of mapped bases = 20,315,137,888 bp number of sequenced bases = 20,301,799,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,962,487 duplication rate = 20.85% >>>>>>> Insert size mean insert size = 84,199.0454 std insert size = 2,949,933.2716 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 54.1165 >>>>>>> ACTG content number of A's = 5,642,206,972 bp (27.79%) number of C's = 4,497,970,402 bp (22.16%) number of T's = 5,538,152,112 bp (27.28%) number of G's = 4,621,215,206 bp (22.76%) number of N's = 2,255,106 bp (0.01%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 150,579,836 number of insertions = 3,291,409 mapped reads with insertion percentage = 1.54% number of deletions = 9,622,993 mapped reads with deletion percentage = 4.47% homopolymer indels = 54.16% >>>>>>> Coverage mean coverageData = 6.5624X std coverageData = 17.8051X There is a 57.11% of reference with a coverageData >= 1X There is a 47.69% of reference with a coverageData >= 2X There is a 39.94% of reference with a coverageData >= 3X There is a 34.59% of reference with a coverageData >= 4X There is a 30.34% of reference with a coverageData >= 5X There is a 26.96% of reference with a coverageData >= 6X There is a 24.17% of reference with a coverageData >= 7X There is a 21.84% of reference with a coverageData >= 8X There is a 19.85% of reference with a coverageData >= 9X There is a 18.15% of reference with a coverageData >= 10X There is a 16.66% of reference with a coverageData >= 11X There is a 15.36% of reference with a coverageData >= 12X There is a 14.21% of reference with a coverageData >= 13X There is a 13.19% of reference with a coverageData >= 14X There is a 12.28% of reference with a coverageData >= 15X There is a 11.46% of reference with a coverageData >= 16X There is a 10.71% of reference with a coverageData >= 17X There is a 10.04% of reference with a coverageData >= 18X There is a 9.43% of reference with a coverageData >= 19X There is a 8.86% of reference with a coverageData >= 20X There is a 8.35% of reference with a coverageData >= 21X There is a 7.88% of reference with a coverageData >= 22X There is a 7.45% of reference with a coverageData >= 23X There is a 7.05% of reference with a coverageData >= 24X There is a 6.68% of reference with a coverageData >= 25X There is a 6.33% of reference with a coverageData >= 26X There is a 6.01% of reference with a coverageData >= 27X There is a 5.71% of reference with a coverageData >= 28X There is a 5.44% of reference with a coverageData >= 29X There is a 5.18% of reference with a coverageData >= 30X There is a 4.94% of reference with a coverageData >= 31X There is a 4.71% of reference with a coverageData >= 32X There is a 4.5% of reference with a coverageData >= 33X There is a 4.3% of reference with a coverageData >= 34X There is a 4.11% of reference with a coverageData >= 35X There is a 3.93% of reference with a coverageData >= 36X There is a 3.76% of reference with a coverageData >= 37X There is a 3.61% of reference with a coverageData >= 38X There is a 3.46% of reference with a coverageData >= 39X There is a 3.32% of reference with a coverageData >= 40X There is a 3.18% of reference with a coverageData >= 41X There is a 3.06% of reference with a coverageData >= 42X There is a 2.94% of reference with a coverageData >= 43X There is a 2.82% of reference with a coverageData >= 44X There is a 2.72% of reference with a coverageData >= 45X There is a 2.61% of reference with a coverageData >= 46X There is a 2.52% of reference with a coverageData >= 47X There is a 2.42% of reference with a coverageData >= 48X There is a 2.34% of reference with a coverageData >= 49X There is a 2.25% of reference with a coverageData >= 50X There is a 2.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1895513598 7.6048500517075945 21.733563219172893 chr2 243199373 1739185989 7.151276615338971 21.601890530092724 chr3 198022430 1326784135 6.700170960431099 15.170067262046587 chr4 191154276 998233158 5.222133550389425 17.498921126591963 chr5 180915260 1152324982 6.369418378527052 14.517571123436007 chr6 171115067 1096652748 6.408861400849055 14.744830738601125 chr7 159138663 852959051 5.3598480401962405 13.073934744711798 chr8 146364022 1022003326 6.982613022208422 16.107430051169047 chr9 141213431 920150076 6.516023790966456 19.92590676357683 chr10 135534747 1052372871 7.764598335805356 18.31402431568685 chr11 135006516 1095651718 8.115546941452811 18.765727670808946 chr12 133851895 948975356 7.089741658121463 16.200820132747264 chr13 115169878 529057259 4.593712072873777 12.109143496368166 chr14 107349540 638883878 5.951435637264957 14.979211112375463 chr15 102531392 672284373 6.556863804209349 15.923301768326345 chr16 90354753 766074195 8.478515734529207 22.754686995683826 chr17 81195210 703800056 8.66799970096758 20.642487306908087 chr18 78077248 527539346 6.756633456138208 20.182980566908874 chr19 59128983 442836839 7.489336303991563 18.93776121107887 chr20 63025520 623649006 9.895182237290545 20.766311767185208 chr21 48129895 263249257 5.469558098973621 30.849323959350812 chr22 51304566 392312992 7.6467461395151455 19.396938225763133 chrMT 16571 3889154 234.69639732062035 181.08996713340954 chrX 155270560 550056325 3.542566762173074 8.744430343034958 chrY 59373566 100698200 1.6960106455455277 11.641173598572767