BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975224.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 128,470,164 number of mapped reads = 128,004,436 (99.64%) number of supplementary alignments = 281,419 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 63,994,164 number of mapped paired reads (second in pair) = 64,010,272 number of mapped paired reads (both in pair) = 127,808,424 number of mapped paired reads (singletons) = 196,012 number of mapped bases = 11,724,822,770 bp number of sequenced bases = 11,720,811,812 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,289,641 duplication rate = 49.78% >>>>>>> Insert size mean insert size = 63,639.4161 std insert size = 2,494,992.6278 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 55.8922 >>>>>>> ACTG content number of A's = 3,153,176,626 bp (26.9%) number of C's = 2,562,838,629 bp (21.87%) number of T's = 3,187,861,787 bp (27.2%) number of G's = 2,816,583,606 bp (24.03%) number of N's = 351,164 bp (0%) GC percentage = 45.9% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 70,655,074 number of insertions = 1,188,150 mapped reads with insertion percentage = 0.92% number of deletions = 2,662,462 mapped reads with deletion percentage = 2.05% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 3.7875X std coverageData = 51.7621X There is a 22.32% of reference with a coverageData >= 1X There is a 13% of reference with a coverageData >= 2X There is a 7.98% of reference with a coverageData >= 3X There is a 5.81% of reference with a coverageData >= 4X There is a 4.42% of reference with a coverageData >= 5X There is a 3.69% of reference with a coverageData >= 6X There is a 3.18% of reference with a coverageData >= 7X There is a 2.86% of reference with a coverageData >= 8X There is a 2.62% of reference with a coverageData >= 9X There is a 2.45% of reference with a coverageData >= 10X There is a 2.32% of reference with a coverageData >= 11X There is a 2.21% of reference with a coverageData >= 12X There is a 2.13% of reference with a coverageData >= 13X There is a 2.05% of reference with a coverageData >= 14X There is a 1.99% of reference with a coverageData >= 15X There is a 1.93% of reference with a coverageData >= 16X There is a 1.88% of reference with a coverageData >= 17X There is a 1.84% of reference with a coverageData >= 18X There is a 1.79% of reference with a coverageData >= 19X There is a 1.76% of reference with a coverageData >= 20X There is a 1.72% of reference with a coverageData >= 21X There is a 1.69% of reference with a coverageData >= 22X There is a 1.65% of reference with a coverageData >= 23X There is a 1.62% of reference with a coverageData >= 24X There is a 1.6% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.52% of reference with a coverageData >= 28X There is a 1.49% of reference with a coverageData >= 29X There is a 1.47% of reference with a coverageData >= 30X There is a 1.45% of reference with a coverageData >= 31X There is a 1.43% of reference with a coverageData >= 32X There is a 1.41% of reference with a coverageData >= 33X There is a 1.39% of reference with a coverageData >= 34X There is a 1.37% of reference with a coverageData >= 35X There is a 1.35% of reference with a coverageData >= 36X There is a 1.34% of reference with a coverageData >= 37X There is a 1.32% of reference with a coverageData >= 38X There is a 1.3% of reference with a coverageData >= 39X There is a 1.29% of reference with a coverageData >= 40X There is a 1.27% of reference with a coverageData >= 41X There is a 1.25% of reference with a coverageData >= 42X There is a 1.24% of reference with a coverageData >= 43X There is a 1.23% of reference with a coverageData >= 44X There is a 1.21% of reference with a coverageData >= 45X There is a 1.2% of reference with a coverageData >= 46X There is a 1.18% of reference with a coverageData >= 47X There is a 1.17% of reference with a coverageData >= 48X There is a 1.16% of reference with a coverageData >= 49X There is a 1.15% of reference with a coverageData >= 50X There is a 1.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1371124168 5.500985965447203 67.06453997557257 chr2 243199373 903257257 3.7140607965300965 48.2599078300569 chr3 198022430 710698023 3.5889773850366344 46.85341697127096 chr4 191154276 425345459 2.225142266762581 34.6287936960975 chr5 180915260 564042207 3.1177149290778456 45.79647395918637 chr6 171115067 779111748 4.553145211929234 60.60289548821252 chr7 159138663 633485729 3.9807154154612947 56.88798975310907 chr8 146364022 488285818 3.336105494559312 44.34750970623406 chr9 141213431 457204751 3.2376860172740933 44.421712910972005 chr10 135534747 460063665 3.3944333477820265 44.015226075060575 chr11 135006516 661572772 4.900302530583042 63.071526551950654 chr12 133851895 649377845 4.851465457399763 61.51770305612049 chr13 115169878 204056308 1.7717853968726094 34.21560642563194 chr14 107349540 369357024 3.440694985744699 45.96902291935674 chr15 102531392 344643210 3.361343324003638 45.99135097355666 chr16 90354753 367680054 4.069293997184631 49.48585615885459 chr17 81195210 607127217 7.477377261540428 74.76599553738642 chr18 78077248 238275746 3.0517948839590248 46.409219820334606 chr19 59128983 635320504 10.744654681444462 101.46322535253874 chr20 63025520 276115455 4.381010343111806 58.26577338320726 chr21 48129895 116609512 2.4228083605833755 41.13252843684023 chr22 51304566 150517746 2.933807996738536 38.842012838504786 chrMT 16571 744902 44.95214531410295 73.75310412861758 chrX 155270560 288469676 1.8578517138084645 28.82284109012817 chrY 59373566 22335974 0.37619391094009746 10.945326429041836