BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006205.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 3,126,044 number of mapped reads = 2,256,281 (72.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,130,937 number of mapped paired reads (second in pair) = 1,125,344 number of mapped paired reads (both in pair) = 2,074,696 number of mapped paired reads (singletons) = 181,585 number of mapped bases = 87,313,477 bp number of sequenced bases = 87,302,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,456 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 57,504.6073 std insert size = 2,330,578.8474 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 47.7984 >>>>>>> ACTG content number of A's = 23,926,695 bp (27.41%) number of C's = 19,112,447 bp (21.89%) number of T's = 24,439,115 bp (27.99%) number of G's = 19,819,452 bp (22.7%) number of N's = 4,337 bp (0%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 253,983 number of insertions = 2,818 mapped reads with insertion percentage = 0.12% number of deletions = 8,603 mapped reads with deletion percentage = 0.38% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2156X There is a 2.46% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 7293325 0.02926101034669037 0.25281017084295904 chr2 243199373 7342414 0.03019092487545188 0.23217674946011282 chr3 198022430 5825785 0.029419823804808374 0.1907329195489234 chr4 191154276 5328152 0.027873569514081913 0.19373365845693696 chr5 180915260 5206352 0.02877784881164806 0.21079058950254748 chr6 171115067 4967552 0.02903047690125382 0.1990407631049658 chr7 159138663 4658192 0.029271277715837037 0.23116523802516634 chr8 146364022 4305355 0.02941539144093758 0.2845660937876251 chr9 141213431 3683214 0.02608260399819901 0.1936326970550683 chr10 135534747 4164273 0.030724763148744432 0.21843237536332896 chr11 135006516 4022895 0.029797783982515334 0.208391687144159 chr12 133851895 3882984 0.02900955567345535 0.18986331496970338 chr13 115169878 2634082 0.022871275421512557 0.16792746690557234 chr14 107349540 2673275 0.024902528692717266 0.2697306966867041 chr15 102531392 2633052 0.02568044721366896 0.1784464496156037 chr16 90354753 2720208 0.030105865045085122 0.2066522741383412 chr17 81195210 2524492 0.031091637055929777 0.20107661120245796 chr18 78077248 2252033 0.02884365237873138 0.24709534904449884 chr19 59128983 1888761 0.03194306589037731 0.23281667022039285 chr20 63025520 1968512 0.03123357014745773 0.19973676005833416 chr21 48129895 1163077 0.024165375802295018 0.2119094557312787 chr22 51304566 1215866 0.023698982269921162 0.19292718372168918 chrMT 16571 1512 0.09124373906221712 0.3810456558437879 chrX 155270560 4749683 0.030589720292114615 0.20098992841396562 chrY 59373566 208431 0.0035105016262624348 0.09393875822866903