BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472533.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 = 22,076,474 number of mapped reads = 21,712,106 (98.35%) number of supplementary alignments = 74,629 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,906,653 number of mapped paired reads (second in pair) = 10,805,453 number of mapped paired reads (both in pair) = 21,530,020 number of mapped paired reads (singletons) = 182,086 number of mapped bases = 2,134,871,685 bp number of sequenced bases = 2,134,598,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,444,414 duplication rate = 45.72% >>>>>>> Insert size mean insert size = 24,390.8833 std insert size = 1,566,793.7447 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.0971 >>>>>>> ACTG content number of A's = 593,469,789 bp (27.8%) number of C's = 477,367,188 bp (22.36%) number of T's = 589,681,578 bp (27.62%) number of G's = 473,749,050 bp (22.19%) number of N's = 331,188 bp (0.02%) GC percentage = 44.56% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 13,271,640 number of insertions = 114,361 mapped reads with insertion percentage = 0.52% number of deletions = 112,948 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.48% >>>>>>> Coverage mean coverageData = 0.6896X std coverageData = 26.5462X There is a 6.62% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 1.35% of reference with a coverageData >= 3X There is a 0.9% of reference with a coverageData >= 4X There is a 0.62% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 261359932 1.048582871935954 37.86577517043005 chr2 243199373 138081084 0.5677690789112355 32.822667822912656 chr3 198022430 208692839 1.053884850317209 24.898450241159154 chr4 191154276 68707832 0.3594365422408861 12.482220025271532 chr5 180915260 109610969 0.6058691179505808 19.57541248179568 chr6 171115067 169990098 0.9934256578352624 33.73081846293872 chr7 159138663 87808393 0.55177284604936 19.6024292375961 chr8 146364022 98143727 0.670545436364136 25.437416062281216 chr9 141213431 165818746 1.1742420308447856 42.58619761386461 chr10 135534747 54955164 0.40546918938801724 19.872363919204872 chr11 135006516 109123246 0.808281327695324 34.90154900842596 chr12 133851895 98951319 0.7392597542231285 24.192312596517233 chr13 115169878 61732954 0.5360164920900585 25.348087211231455 chr14 107349540 53282710 0.49634781853746185 19.595557402666785 chr15 102531392 55984124 0.5460193498592119 19.10675643246301 chr16 90354753 87957609 0.9734696413812343 31.735063547073924 chr17 81195210 82007811 1.0100079918507507 26.229839163706053 chr18 78077248 35890829 0.4596835815729571 19.20507878161032 chr19 59128983 34862613 0.5896027841371803 20.51833177584973 chr20 63025520 37053837 0.5879179894112734 19.475206726385455 chr21 48129895 6765327 0.14056392601729134 5.1788946661195245 chr22 51304566 15443412 0.30101437755072324 9.577729793694433 chrMT 16571 2108 0.12721018647033974 0.4554791799652792 chrX 155270560 88723325 0.5714111226236319 18.428174548413434 chrY 59373566 3921677 0.06605089207543977 4.605931736001814