BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124905.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,566,480 number of mapped reads = 3,520,600 (98.71%) number of supplementary alignments = 38,776 (1.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,764,546 number of mapped paired reads (second in pair) = 1,756,054 number of mapped paired reads (both in pair) = 3,505,722 number of mapped paired reads (singletons) = 14,878 number of mapped bases = 473,853,041 bp number of sequenced bases = 473,553,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 521,184 duplication rate = 14.13% >>>>>>> Insert size mean insert size = 73,982.2146 std insert size = 2,631,864.3464 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.6966 >>>>>>> ACTG content number of A's = 137,918,610 bp (29.12%) number of C's = 95,800,499 bp (20.23%) number of T's = 139,284,191 bp (29.41%) number of G's = 100,529,292 bp (21.23%) number of N's = 20,409 bp (0%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 6,390,558 number of insertions = 80,700 mapped reads with insertion percentage = 2.2% number of deletions = 163,756 mapped reads with deletion percentage = 4.5% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.1531X std coverageData = 1.909X There is a 7.96% of reference with a coverageData >= 1X There is a 4.73% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% 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 44751931 0.1795459157552109 2.94729117759382 chr2 243199373 37094410 0.15252675014092246 1.632379593814548 chr3 198022430 32255700 0.16288912321700122 0.655894205319695 chr4 191154276 23762351 0.12430980617980003 0.7938090740520973 chr5 180915260 31254292 0.17275652700606903 0.6042392051895241 chr6 171115067 29351690 0.1715318850326605 1.238119082407887 chr7 159138663 41722366 0.262176175251642 2.72377738182144 chr8 146364022 40250480 0.2750025549311565 1.1018658497353655 chr9 141213431 19348527 0.13701619501051568 2.0991172544468952 chr10 135534747 20571628 0.15178121076213763 5.616574258168439 chr11 135006516 19002103 0.14074952500811147 1.2403474297083112 chr12 133851895 11758083 0.08784397860037768 0.4257681048749437 chr13 115169878 21782552 0.18913410674968328 0.6719608310941276 chr14 107349540 9774417 0.09105224857041772 0.4744191620874642 chr15 102531392 7085613 0.06910676683293249 0.380910043869378 chr16 90354753 8490791 0.09397171391747372 1.2827246613508851 chr17 81195210 12580471 0.15494104886236515 2.248355305196021 chr18 78077248 12886213 0.16504440576594093 2.309148445351041 chr19 59128983 11014000 0.18627074982838787 1.6708200790781973 chr20 63025520 11903772 0.18887225365217136 0.6941587340092791 chr21 48129895 6769815 0.14065717367552952 0.6889328101012765 chr22 51304566 4200760 0.08187887214560981 0.4141357919424046 chrMT 16571 33730 2.0354836763019732 2.248224592727912 chrX 155270560 12262542 0.07897531895292964 0.560808673316915 chrY 59373566 3944804 0.06644040885130599 1.2658992859330078