BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777284.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 = 138,993,724 number of mapped reads = 137,145,857 (98.67%) number of supplementary alignments = 548,330 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68,753,946 number of mapped paired reads (second in pair) = 68,391,911 number of mapped paired reads (both in pair) = 136,488,978 number of mapped paired reads (singletons) = 656,879 number of mapped bases = 13,336,305,397 bp number of sequenced bases = 13,332,194,081 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,956,661 duplication rate = 8.06% >>>>>>> Insert size mean insert size = 115,315.182 std insert size = 3,318,099.2408 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.5552 >>>>>>> ACTG content number of A's = 3,878,933,872 bp (29.09%) number of C's = 2,788,730,972 bp (20.92%) number of T's = 3,829,527,191 bp (28.72%) number of G's = 2,834,499,079 bp (21.26%) number of N's = 502,967 bp (0%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 67,369,269 number of insertions = 1,388,921 mapped reads with insertion percentage = 0.98% number of deletions = 1,783,624 mapped reads with deletion percentage = 1.27% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 4.308X std coverageData = 52.6393X There is a 88.29% of reference with a coverageData >= 1X There is a 80.07% of reference with a coverageData >= 2X There is a 68.03% of reference with a coverageData >= 3X There is a 54.15% of reference with a coverageData >= 4X There is a 40.41% of reference with a coverageData >= 5X There is a 28.41% of reference with a coverageData >= 6X There is a 18.91% of reference with a coverageData >= 7X There is a 11.99% of reference with a coverageData >= 8X There is a 7.3% of reference with a coverageData >= 9X There is a 4.31% of reference with a coverageData >= 10X There is a 2.5% of reference with a coverageData >= 11X There is a 1.45% of reference with a coverageData >= 12X There is a 0.86% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1115489469 4.475372877807193 123.82256327641723 chr2 243199373 1143148437 4.700457994190635 32.54360397898201 chr3 198022430 887265286 4.480630229615907 11.18601906376546 chr4 191154276 860820006 4.503273607125587 34.601796167919815 chr5 180915260 791772132 4.376480635187988 4.976641976863794 chr6 171115067 763321149 4.4608646239199965 27.573804755652645 chr7 159138663 728123188 4.575400938237115 44.62739690137454 chr8 146364022 666833479 4.555993131973375 16.011019523445924 chr9 141213431 573904039 4.064089619067467 48.32460640846514 chr10 135534747 738828283 5.451209371424141 137.33126200967425 chr11 135006516 625793351 4.635282574064796 28.47888464813541 chr12 133851895 599824822 4.481257601918897 4.623838078645632 chr13 115169878 406985602 3.5337851273924246 3.05067157407222 chr14 107349540 404162262 3.7649184337445694 5.012062266362117 chr15 102531392 385389216 3.7587436245867023 3.2900304139078203 chr16 90354753 424721776 4.7006024796504065 22.439581066633377 chr17 81195210 396635404 4.884960627603525 28.82683620535349 chr18 78077248 368239672 4.716350555798278 60.74179835774227 chr19 59128983 290013417 4.904759092507984 57.53982674654639 chr20 63025520 298915825 4.742774434863845 9.565461502407384 chr21 48129895 186351582 3.8718468427990547 16.011579755764462 chr22 51304566 175052333 3.412022489382329 6.851770511933245 chrMT 16571 14831073 895.0016896988715 92.20255629927424 chrX 155270560 358828877 2.310991066175069 12.998255912611079 chrY 59373566 131054717 2.2072906485017256 39.91882448231558