BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975307.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 = 62,855,282 number of mapped reads = 62,611,270 (99.61%) number of supplementary alignments = 129,324 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,285,768 number of mapped paired reads (second in pair) = 31,325,502 number of mapped paired reads (both in pair) = 62,488,234 number of mapped paired reads (singletons) = 123,036 number of mapped bases = 5,639,560,740 bp number of sequenced bases = 5,637,514,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,207,806 duplication rate = 42.23% >>>>>>> Insert size mean insert size = 67,417.3099 std insert size = 2,560,120.1161 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 55.4967 >>>>>>> ACTG content number of A's = 1,490,513,416 bp (26.44%) number of C's = 1,226,291,878 bp (21.75%) number of T's = 1,510,684,901 bp (26.8%) number of G's = 1,409,921,597 bp (25.01%) number of N's = 102,558 bp (0%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 33,461,431 number of insertions = 619,683 mapped reads with insertion percentage = 0.98% number of deletions = 1,355,894 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 1.8217X std coverageData = 27.5214X There is a 17.64% of reference with a coverageData >= 1X There is a 10.2% of reference with a coverageData >= 2X There is a 6.12% of reference with a coverageData >= 3X There is a 4.33% of reference with a coverageData >= 4X There is a 3.17% of reference with a coverageData >= 5X There is a 2.56% of reference with a coverageData >= 6X There is a 2.13% of reference with a coverageData >= 7X There is a 1.86% of reference with a coverageData >= 8X There is a 1.67% of reference with a coverageData >= 9X There is a 1.54% of reference with a coverageData >= 10X There is a 1.43% of reference with a coverageData >= 11X There is a 1.35% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.23% of reference with a coverageData >= 14X There is a 1.19% of reference with a coverageData >= 15X There is a 1.15% of reference with a coverageData >= 16X There is a 1.11% of reference with a coverageData >= 17X There is a 1.08% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 1.02% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.97% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.89% of reference with a coverageData >= 26X There is a 0.87% of reference with a coverageData >= 27X There is a 0.86% of reference with a coverageData >= 28X There is a 0.84% of reference with a coverageData >= 29X There is a 0.83% of reference with a coverageData >= 30X There is a 0.81% of reference with a coverageData >= 31X There is a 0.8% of reference with a coverageData >= 32X There is a 0.78% of reference with a coverageData >= 33X There is a 0.77% of reference with a coverageData >= 34X There is a 0.76% of reference with a coverageData >= 35X There is a 0.74% of reference with a coverageData >= 36X There is a 0.73% of reference with a coverageData >= 37X There is a 0.72% of reference with a coverageData >= 38X There is a 0.71% of reference with a coverageData >= 39X There is a 0.7% of reference with a coverageData >= 40X There is a 0.69% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.67% of reference with a coverageData >= 43X There is a 0.66% of reference with a coverageData >= 44X There is a 0.65% of reference with a coverageData >= 45X There is a 0.64% of reference with a coverageData >= 46X There is a 0.63% of reference with a coverageData >= 47X There is a 0.62% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.61% of reference with a coverageData >= 50X There is a 0.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 685467522 2.750113597510355 37.19970630912267 chr2 243199373 413215522 1.699081362352032 23.81719160504398 chr3 198022430 275629885 1.3919124464839665 20.557722702611585 chr4 191154276 245477855 1.2841870981740424 19.632177806697715 chr5 180915260 271611154 1.5013169922758312 21.17421058238701 chr6 171115067 458191271 2.6776792893404298 40.395371880672705 chr7 159138663 301937052 1.897320527318996 31.72978405988905 chr8 146364022 200821701 1.3720701184338868 19.155664226994833 chr9 141213431 233355122 1.6524994849817083 23.50432322489332 chr10 135534747 235934228 1.7407656207894793 25.46442393984601 chr11 135006516 261012001 1.9333289142873666 27.90007730740281 chr12 133851895 316862355 2.3672608818874026 31.27828976858283 chr13 115169878 120754713 1.0484921500047086 18.027346322588787 chr14 107349540 189084759 1.7613932858957757 26.52561781432149 chr15 102531392 204760483 1.9970516249306358 29.21134200534797 chr16 90354753 184817735 2.0454677685854556 27.236992319580306 chr17 81195210 220915951 2.7208002910516518 33.362837698326516 chr18 78077248 106545077 1.364611070820529 20.21707791956425 chr19 59128983 242493412 4.1010922173310504 50.44115900823205 chr20 63025520 149869769 2.377921975098341 30.833837724348776 chr21 48129895 60659815 1.2603354941871368 28.31968855395975 chr22 51304566 96093897 1.873008671391938 28.266266256797735 chrMT 16571 420729 25.389475589885944 25.13592413005089 chrX 155270560 147444500 0.9495972707253713 17.170663364144772 chrY 59373566 16184232 0.2725831222601654 5.041393927751074