BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472403.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,409,886 number of mapped reads = 16,272,612 (99.16%) number of supplementary alignments = 58,392 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,161,380 number of mapped paired reads (second in pair) = 8,111,232 number of mapped paired reads (both in pair) = 16,185,854 number of mapped paired reads (singletons) = 86,758 number of mapped bases = 1,597,890,496 bp number of sequenced bases = 1,597,708,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,016,825 duplication rate = 47.03% >>>>>>> Insert size mean insert size = 18,326.4042 std insert size = 1,337,869.7299 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 55.2186 >>>>>>> ACTG content number of A's = 430,352,956 bp (26.94%) number of C's = 369,426,077 bp (23.12%) number of T's = 431,960,602 bp (27.04%) number of G's = 365,776,368 bp (22.89%) number of N's = 192,501 bp (0.01%) GC percentage = 46.02% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 8,721,478 number of insertions = 96,139 mapped reads with insertion percentage = 0.58% number of deletions = 78,014 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.5162X std coverageData = 15.982X There is a 4.39% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211145566 0.8471215243231028 23.850641765776647 chr2 243199373 115558604 0.4751599585743998 16.30087533493542 chr3 198022430 132187013 0.6675355564518626 15.214824303857409 chr4 191154276 65877759 0.3446313646679816 13.0928933524455 chr5 180915260 94732572 0.5236295268845756 20.09004897238356 chr6 171115067 102664789 0.5999751558990419 13.210666306265646 chr7 159138663 89875513 0.5647622727608312 17.02243447819167 chr8 146364022 95483092 0.6523672327069558 18.69880295660596 chr9 141213431 68692277 0.4864429432353357 13.881924702008723 chr10 135534747 39072304 0.28828256122394946 8.915867741309874 chr11 135006516 56475875 0.4183196239209669 13.374284453098191 chr12 133851895 61659961 0.4606581102195079 10.435081791022935 chr13 115169878 25934609 0.22518569482204365 6.4639567070511 chr14 107349540 65018911 0.6056747984201889 21.93666153613684 chr15 102531392 32667466 0.31860940696094325 9.054180675250548 chr16 90354753 67465650 0.7466751638400251 17.84766371471779 chr17 81195210 78361821 0.965103988277141 25.639967343866413 chr18 78077248 27355586 0.35036565325663116 11.180602500133881 chr19 59128983 44786044 0.7574296348036292 15.122711402741013 chr20 63025520 25612655 0.4063854610005598 12.101572432427293 chr21 48129895 9545916 0.19833652244618444 10.544358577917817 chr22 51304566 21680447 0.422583186845397 13.590085266940177 chrMT 16571 2887 0.17422002293162756 0.5452228218996981 chrX 155270560 64094888 0.4127948530616493 14.847988369615015 chrY 59373566 1938291 0.03264568949757877 1.2709605867244098