BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 481,778 number of mapped reads = 457,082 (94.87%) number of supplementary alignments = 6,150 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 229,479 number of mapped paired reads (second in pair) = 227,603 number of mapped paired reads (both in pair) = 454,278 number of mapped paired reads (singletons) = 2,804 number of mapped bases = 63,475,140 bp number of sequenced bases = 63,088,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 452,559 duplication rate = 43.63% >>>>>>> Insert size mean insert size = 135,413.7985 std insert size = 3,878,402.7996 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 31.6931 >>>>>>> ACTG content number of A's = 17,351,098 bp (27.5%) number of C's = 14,039,873 bp (22.25%) number of T's = 17,076,265 bp (27.07%) number of G's = 14,620,540 bp (23.17%) number of N's = 725 bp (0%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0257 number of mismatches = 1,403,648 number of insertions = 57,743 mapped reads with insertion percentage = 12.54% number of deletions = 96,208 mapped reads with deletion percentage = 19.64% homopolymer indels = 34.52% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 21.0765X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 308377 0.0012372165764834744 0.6259740064345632 chr2 243199373 3433284 0.014117158106324558 10.77682915824168 chr3 198022430 83258 4.2044732003339216E-4 0.2938395969196886 chr4 191154276 160278 8.384745732813217E-4 0.48036218609016107 chr5 180915260 1330334 0.007353354272049798 5.073292877044315 chr6 171115067 2984466 0.017441281193549135 17.326364089779 chr7 159138663 181913 0.0011431100184623269 0.5475599336308662 chr8 146364022 193177 0.0013198393796530134 0.5895112277687785 chr9 141213431 56701 4.015269624034558E-4 0.11860614541408612 chr10 135534747 177880 0.0013124309738815538 0.4814083984901078 chr11 135006516 44376 3.286952460872333E-4 0.0841116925006619 chr12 133851895 895691 0.006691657223082273 3.4994948697495865 chr13 115169878 496300 0.004309286495901298 2.665215480200092 chr14 107349540 63248 5.891781185089382E-4 0.21577108344342327 chr15 102531392 73091 7.128646024819403E-4 0.2684553227182147 chr16 90354753 261058 0.002889255864602939 1.944749218625433 chr17 81195210 145985 0.0017979508889748546 0.6742925294916705 chr18 78077248 87857 0.0011252573861209863 0.43613863744283915 chr19 59128983 19228 3.251873958325987E-4 0.05623796820571889 chr20 63025520 257559 0.0040865827049106455 1.842135405175487 chr21 48129895 12587 2.615214514804157E-4 0.06113343570503847 chr22 51304566 15008 2.925275695734372E-4 0.09521681572695567 chrMT 16571 31629277 1908.7126304990647 7866.974674988153 chrX 155270560 20535682 0.13225740926032598 36.040147550940894 chrY 59373566 28525 4.804326558387953E-4 0.25465243242178476