BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975323.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,476,888 number of mapped reads = 4,430,810 (98.97%) number of supplementary alignments = 27,198 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,214,572 number of mapped paired reads (second in pair) = 2,216,238 number of mapped paired reads (both in pair) = 4,415,640 number of mapped paired reads (singletons) = 15,170 number of mapped bases = 416,221,990 bp number of sequenced bases = 415,980,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,537 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 95,038.4554 std insert size = 2,923,402.9545 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.7038 >>>>>>> ACTG content number of A's = 121,835,331 bp (29.29%) number of C's = 84,484,881 bp (20.31%) number of T's = 122,968,254 bp (29.56%) number of G's = 86,683,698 bp (20.84%) number of N's = 8,579 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 3,186,630 number of insertions = 71,120 mapped reads with insertion percentage = 1.57% number of deletions = 139,818 mapped reads with deletion percentage = 3.09% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.1345X std coverageData = 2.3347X There is a 9.06% of reference with a coverageData >= 1X There is a 2.65% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 39361447 0.15791915318838864 1.7976417357097634 chr2 243199373 24310099 0.09995954635952124 1.5273915636149733 chr3 198022430 17759113 0.08968233043095168 0.6318684393179314 chr4 191154276 25528489 0.13354913912571853 1.3128778939924421 chr5 180915260 23615733 0.1305347763367225 0.4763663114104454 chr6 171115067 27510209 0.16077023188145087 1.6835512370081567 chr7 159138663 20214257 0.12702291585797726 1.9137512124638842 chr8 146364022 32341225 0.22096430911142903 0.8434024076124711 chr9 141213431 15818255 0.11201664663186323 1.7727839806079977 chr10 135534747 24744699 0.18257088715412587 9.28004367322346 chr11 135006516 18350710 0.13592462455663992 1.5782904269110516 chr12 133851895 22128503 0.16532080475961883 0.5300623500441916 chr13 115169878 12683591 0.11012941248405247 0.42375778936404723 chr14 107349540 22334596 0.20805488314155796 0.6343046704307079 chr15 102531392 6921229 0.06750351150991883 0.32443158402680927 chr16 90354753 9516298 0.10532149869304606 1.95110262758295 chr17 81195210 8174665 0.10067915336384992 1.4830403235127332 chr18 78077248 20404586 0.26133843754329045 2.520416674039918 chr19 59128983 4575537 0.07738230505334415 0.958790253545571 chr20 63025520 5410051 0.08583905376742627 0.48156423339638654 chr21 48129895 6159461 0.1279757830346399 0.685928335738761 chr22 51304566 3550317 0.06920079978846327 0.34164049295983384 chrMT 16571 88243 5.3251463399915515 6.45614251365237 chrX 155270560 23529547 0.1515390103571469 0.835679629411125 chrY 59373566 1191130 0.0200616213619374 1.1866249473797452