BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960897.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 217,957,998 number of mapped reads = 214,530,156 (98.43%) number of supplementary alignments = 386,707 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 107,475,627 number of mapped paired reads (second in pair) = 107,054,529 number of mapped paired reads (both in pair) = 213,397,106 number of mapped paired reads (singletons) = 1,133,050 number of mapped bases = 21,104,449,243 bp number of sequenced bases = 21,098,280,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,591,989 duplication rate = 9.53% >>>>>>> Insert size mean insert size = 15,709.8972 std insert size = 1,177,054.5624 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.6374 >>>>>>> ACTG content number of A's = 6,460,033,116 bp (30.62%) number of C's = 4,095,425,718 bp (19.41%) number of T's = 6,451,515,212 bp (30.58%) number of G's = 4,090,195,793 bp (19.39%) number of N's = 1,110,278 bp (0.01%) GC percentage = 38.8% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 245,283,909 number of insertions = 2,492,040 mapped reads with insertion percentage = 1.13% number of deletions = 2,630,625 mapped reads with deletion percentage = 1.19% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 6.8174X std coverageData = 93.4595X There is a 89.11% of reference with a coverageData >= 1X There is a 84.58% of reference with a coverageData >= 2X There is a 78.06% of reference with a coverageData >= 3X There is a 70.15% of reference with a coverageData >= 4X There is a 61.46% of reference with a coverageData >= 5X There is a 52.64% of reference with a coverageData >= 6X There is a 44.18% of reference with a coverageData >= 7X There is a 36.39% of reference with a coverageData >= 8X There is a 29.47% of reference with a coverageData >= 9X There is a 23.49% of reference with a coverageData >= 10X There is a 18.46% of reference with a coverageData >= 11X There is a 14.31% of reference with a coverageData >= 12X There is a 10.95% of reference with a coverageData >= 13X There is a 8.29% of reference with a coverageData >= 14X There is a 6.22% of reference with a coverageData >= 15X There is a 4.63% of reference with a coverageData >= 16X There is a 3.43% of reference with a coverageData >= 17X There is a 2.53% of reference with a coverageData >= 18X There is a 1.87% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.03% of reference with a coverageData >= 21X There is a 0.78% of reference with a coverageData >= 22X There is a 0.6% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1786346123 7.166867291375776 231.64913780790855 chr2 243199373 2220494290 9.130345455290298 49.83939185804517 chr3 198022430 1389846534 7.018631848927417 14.048372988553169 chr4 191154276 1179593475 6.1708976627862615 76.36533015266504 chr5 180915260 1142405921 6.31459126775707 8.070863816470057 chr6 171115067 1294461593 7.564860393035992 27.18647617473725 chr7 159138663 1095052258 6.881120133578099 58.70722682304175 chr8 146364022 1207936109 8.252957881958176 96.69166252032257 chr9 141213431 1067833034 7.561837613024217 76.59210969312836 chr10 135534747 939147900 6.929203918460851 220.27162751414522 chr11 135006516 934765383 6.923853830877318 36.277030571586465 chr12 133851895 1066897335 7.9707301491697224 7.760257773598201 chr13 115169878 593927250 5.156966911087637 4.63924615894843 chr14 107349540 419396122 3.9068273790460584 6.817051247779959 chr15 102531392 513980303 5.012906710561386 4.557704079084147 chr16 90354753 570716463 6.316396692490543 85.12110944910324 chr17 81195210 445982252 5.492716282155068 23.903086330493544 chr18 78077248 667193894 8.545304952346681 79.99746943443002 chr19 59128983 362606763 6.132470822303844 101.31416285177076 chr20 63025520 406303834 6.446655799111217 22.157531532939682 chr21 48129895 263940540 5.4839209601433785 30.336900907950834 chr22 51304566 239413303 4.66651063766917 6.093685142973205 chrMT 16571 8239237 497.20819503952686 107.53350295505788 chrX 155270560 1229018039 7.915332043627588 25.388513225529504 chrY 59373566 58951288 0.9928877777022859 65.68903724374675