BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960892.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 = 221,864,044 number of mapped reads = 218,000,068 (98.26%) number of supplementary alignments = 387,457 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 109,234,779 number of mapped paired reads (second in pair) = 108,765,289 number of mapped paired reads (both in pair) = 216,826,398 number of mapped paired reads (singletons) = 1,173,670 number of mapped bases = 21,445,851,804 bp number of sequenced bases = 21,439,554,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,220,960 duplication rate = 9.63% >>>>>>> Insert size mean insert size = 15,329.6507 std insert size = 1,161,794.4308 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.6384 >>>>>>> ACTG content number of A's = 6,550,621,950 bp (30.55%) number of C's = 4,175,004,617 bp (19.47%) number of T's = 6,539,363,396 bp (30.5%) number of G's = 4,174,094,355 bp (19.47%) number of N's = 470,034 bp (0%) GC percentage = 38.94% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 249,442,492 number of insertions = 2,569,261 mapped reads with insertion percentage = 1.15% number of deletions = 2,708,700 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 6.9276X std coverageData = 94.1734X There is a 89.36% of reference with a coverageData >= 1X There is a 85.11% of reference with a coverageData >= 2X There is a 78.83% of reference with a coverageData >= 3X There is a 71.1% of reference with a coverageData >= 4X There is a 62.51% of reference with a coverageData >= 5X There is a 53.7% of reference with a coverageData >= 6X There is a 45.18% of reference with a coverageData >= 7X There is a 37.3% of reference with a coverageData >= 8X There is a 30.27% of reference with a coverageData >= 9X There is a 24.18% of reference with a coverageData >= 10X There is a 19.03% of reference with a coverageData >= 11X There is a 14.77% of reference with a coverageData >= 12X There is a 11.33% of reference with a coverageData >= 13X There is a 8.59% of reference with a coverageData >= 14X There is a 6.45% of reference with a coverageData >= 15X There is a 4.81% of reference with a coverageData >= 16X There is a 3.57% of reference with a coverageData >= 17X There is a 2.64% of reference with a coverageData >= 18X There is a 1.95% of reference with a coverageData >= 19X There is a 1.44% of reference with a coverageData >= 20X There is a 1.08% of reference with a coverageData >= 21X There is a 0.81% of reference with a coverageData >= 22X There is a 0.62% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% 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 0.1% 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 0.08% 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 1818900523 7.297476394251391 234.38211030720245 chr2 243199373 2253322160 9.265328821386394 50.27921127908081 chr3 198022430 1408537471 7.113019828107351 14.194308433635905 chr4 191154276 1193827167 6.245359465565918 76.66839929651947 chr5 180915260 1158664602 6.404460309207748 8.13471844984273 chr6 171115067 1313519967 7.67623792590982 27.416477602854865 chr7 159138663 1111084893 6.981866455670801 58.93730178439425 chr8 146364022 1225833923 8.375240761011609 95.48075927501795 chr9 141213431 1085763025 7.688808474598992 76.73018305733271 chr10 135534747 953786289 7.03720861337499 221.39071312791933 chr11 135006516 949847514 7.035567927699134 36.4633713835546 chr12 133851895 1083737232 8.096540075133042 7.86880363085204 chr13 115169878 602760900 5.233667956129987 4.68600357083461 chr14 107349540 426393513 3.9720106206323753 6.8224661705130725 chr15 102531392 524206378 5.112642750427108 4.5809548011331245 chr16 90354753 581729049 6.438278338274025 85.28151743494742 chr17 81195210 458585467 5.6479374460636285 24.270203656136943 chr18 78077248 676402521 8.66324746743123 80.16945202803386 chr19 59128983 373864196 6.322858554830885 102.66406013873159 chr20 63025520 415414940 6.591217970117501 22.198548085869923 chr21 48129895 268381466 5.57619055682544 30.966700334139123 chr22 51304566 247454606 4.8232472330045635 6.162986977089821 chrMT 16571 8444813 509.61396415424537 106.5172065758693 chrX 155270560 1245270558 8.020004294439332 25.684411114215504 chrY 59373566 60118631 1.0125487662304131 66.33639066987907