BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504758.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 1,935,094 number of mapped reads = 1,720,640 (88.92%) number of secondary alignments = 0 number of mapped bases = 55,054,942 bp number of sequenced bases = 55,054,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 388,905 duplication rate = 12.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.1854 >>>>>>> ACTG content number of A's = 15,802,766 bp (28.7%) number of C's = 11,212,799 bp (20.37%) number of T's = 16,682,194 bp (30.3%) number of G's = 11,356,812 bp (20.63%) number of N's = 371 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0004 number of mismatches = 24,013 >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.8305X There is a 0.78% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3927410 0.015756871474354322 0.5742348117194441 chr2 243199373 4216862 0.017339115426091168 0.5322371052201689 chr3 198022430 4459862 0.02252200419922127 0.49683331693190114 chr4 191154276 3705370 0.019384185787191074 0.6786800396437572 chr5 180915260 3477738 0.01922302187222902 0.38839767617132426 chr6 171115067 3055628 0.017857153397251687 0.5369671028491935 chr7 159138663 2158254 0.0135620971001874 0.3072797965769901 chr8 146364022 7345696 0.05018785285908582 2.9467865336475394 chr9 141213431 1479784 0.010479059884891544 0.18688807887175118 chr10 135534747 2230416 0.01645641467866539 0.3701890174788172 chr11 135006516 3116690 0.02308547833350503 1.0481011959536006 chr12 133851895 3143158 0.023482357123147193 0.5800165502447755 chr13 115169878 1470466 0.012767800274998988 0.2028462575015765 chr14 107349540 3085706 0.0287444734276458 1.1930100085096973 chr15 102531392 1003114 0.009783481726259993 0.17114610930161334 chr16 90354753 2027834 0.02244302521639343 0.9481044776787882 chr17 81195210 967914 0.011920826364018271 0.30353985055046395 chr18 78077248 803890 0.010296085230872892 0.16682707037566316 chr19 59128983 554260 0.009373744851995847 0.2510862794073059 chr20 63025520 796228 0.012633422143918844 0.25116291564289234 chr21 48129895 400634 0.00832401566635456 0.1877947752446183 chr22 51304566 233140 0.004544234912736617 0.12135294132638494 chrMT 16571 0 0.0 0.0 chrX 155270560 857998 0.005525825372176155 0.12151802185652448 chrY 59373566 536890 0.009042576287231931 0.23881133406800223