BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472561.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 = 10,109,246 number of mapped reads = 9,910,971 (98.04%) number of supplementary alignments = 44,947 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,975,333 number of mapped paired reads (second in pair) = 4,935,638 number of mapped paired reads (both in pair) = 9,820,308 number of mapped paired reads (singletons) = 90,663 number of mapped bases = 970,352,458 bp number of sequenced bases = 970,230,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,833,245 duplication rate = 43.14% >>>>>>> Insert size mean insert size = 37,886.5382 std insert size = 1,890,470.7265 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 54.5781 >>>>>>> ACTG content number of A's = 271,380,349 bp (27.97%) number of C's = 215,355,831 bp (22.2%) number of T's = 268,871,085 bp (27.71%) number of G's = 214,473,416 bp (22.11%) number of N's = 149,443 bp (0.02%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 6,201,787 number of insertions = 58,475 mapped reads with insertion percentage = 0.58% number of deletions = 54,779 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.3135X std coverageData = 14.0669X There is a 3.36% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.13% 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 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 92061204 0.36935195439292406 20.095279553166126 chr2 243199373 53941370 0.22179896820704387 7.859231563195906 chr3 198022430 135956772 0.6865725867519149 17.992824993608235 chr4 191154276 40654076 0.21267678050790764 7.918421082802737 chr5 180915260 42824616 0.23671091095355914 9.211253141529216 chr6 171115067 71812892 0.41967603004824816 16.850565397274405 chr7 159138663 49186458 0.30907924619173155 13.257192080089077 chr8 146364022 49028309 0.33497514163692493 16.899882332342514 chr9 141213431 65914658 0.4667732915575148 15.596565971432632 chr10 135534747 28440983 0.2098427423928419 9.472092612339955 chr11 135006516 36094162 0.2673512588088711 9.146656285573375 chr12 133851895 41484758 0.30993030020232437 10.102435135165745 chr13 115169878 21104239 0.18324443306261035 7.07454317434012 chr14 107349540 22783045 0.21223234864350607 28.495245432261576 chr15 102531392 17778785 0.17339845537257506 5.147539759309355 chr16 90354753 22558219 0.24966278199000777 7.204475376474502 chr17 81195210 41298406 0.5086310633348937 16.77093363715481 chr18 78077248 20887974 0.26752958813302435 14.206981073516305 chr19 59128983 24681147 0.4174119991206343 16.589848107395195 chr20 63025520 33314085 0.5285808827916056 25.80793123494292 chr21 48129895 3325999 0.06910463860351243 2.2656942719520567 chr22 51304566 9984826 0.1946186622064009 8.169961266568324 chrMT 16571 1987 0.11990827348983163 0.44792430984478937 chrX 155270560 44941095 0.2894373215373217 9.729353944001602 chrY 59373566 292393 0.00492463262186408 0.3570111926016298