BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472540.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 = 16,204,788 number of mapped reads = 15,970,720 (98.56%) number of supplementary alignments = 70,412 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,014,113 number of mapped paired reads (second in pair) = 7,956,607 number of mapped paired reads (both in pair) = 15,866,026 number of mapped paired reads (singletons) = 104,694 number of mapped bases = 1,572,340,171 bp number of sequenced bases = 1,572,129,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,005,919 duplication rate = 44.65% >>>>>>> Insert size mean insert size = 32,763.7272 std insert size = 1,802,164.5356 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 55.0672 >>>>>>> ACTG content number of A's = 435,841,749 bp (27.72%) number of C's = 352,768,086 bp (22.44%) number of T's = 433,189,397 bp (27.55%) number of G's = 350,088,574 bp (22.27%) number of N's = 242,075 bp (0.02%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,748,326 number of insertions = 84,222 mapped reads with insertion percentage = 0.52% number of deletions = 89,529 mapped reads with deletion percentage = 0.55% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.5079X std coverageData = 18.2099X There is a 5.41% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 185734010 0.7451696980927481 25.747507602725555 chr2 243199373 118114970 0.48567135902936726 18.03094933021235 chr3 198022430 195707283 0.9883086628115815 24.568850967700282 chr4 191154276 64569970 0.3377898279398155 12.355988269119752 chr5 180915260 71168824 0.39338209502061905 13.20841266829602 chr6 171115067 78374854 0.4580242720531442 14.24530525641307 chr7 159138663 80703987 0.5071299800979225 17.091517467392123 chr8 146364022 72788440 0.49731101267495914 19.113140645803746 chr9 141213431 96731300 0.6850007064837905 19.957565904097827 chr10 135534747 50155215 0.37005429316218075 17.399570775291892 chr11 135006516 89446726 0.6625363623189862 26.201691452476595 chr12 133851895 79306627 0.5924953621314065 19.38506538921534 chr13 115169878 39422487 0.3422985913035351 16.011291161739695 chr14 107349540 37825530 0.352358566231397 14.359293813364935 chr15 102531392 35823065 0.3493863128279776 10.152249872222264 chr16 90354753 50014170 0.5535311462807053 19.85338932051432 chr17 81195210 45687266 0.5626842519404778 18.821602836192934 chr18 78077248 29212142 0.37414410405448717 13.692440207388936 chr19 59128983 18510137 0.31304676760633615 10.329746026874785 chr20 63025520 24222210 0.3843238421515602 12.225612922499572 chr21 48129895 7627298 0.15847319010357283 9.233484550628303 chr22 51304566 10534807 0.20533858526354165 8.969398716065955 chrMT 16571 5517 0.3329310240782089 1.075982526672255 chrX 155270560 88394059 0.5692905274509218 19.904654289525073 chrY 59373566 2259277 0.038051900066100125 1.6907504310323243