BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006146.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 = 27,919,118 number of mapped reads = 23,233,576 (83.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,840,556 number of mapped paired reads (second in pair) = 11,393,020 number of mapped paired reads (both in pair) = 20,544,472 number of mapped paired reads (singletons) = 2,689,104 number of mapped bases = 892,601,504 bp number of sequenced bases = 892,500,634 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,879,072 duplication rate = 25.71% >>>>>>> Insert size mean insert size = 87,024.4387 std insert size = 2,935,242.0554 median insert size = 82 >>>>>>> Mapping quality mean mapping quality = 45.1892 >>>>>>> ACTG content number of A's = 237,148,542 bp (26.57%) number of C's = 197,443,091 bp (22.12%) number of T's = 247,250,104 bp (27.7%) number of G's = 210,625,513 bp (23.6%) number of N's = 33,384 bp (0%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 4,419,918 number of insertions = 34,678 mapped reads with insertion percentage = 0.15% number of deletions = 79,753 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.2883X std coverageData = 2.1684X There is a 4.91% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 2.67% of reference with a coverageData >= 3X There is a 2.3% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.78% of reference with a coverageData >= 6X There is a 1.57% of reference with a coverageData >= 7X There is a 1.39% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 1.08% of reference with a coverageData >= 10X There is a 0.94% of reference with a coverageData >= 11X There is a 0.82% of reference with a coverageData >= 12X There is a 0.71% of reference with a coverageData >= 13X There is a 0.6% of reference with a coverageData >= 14X There is a 0.52% of reference with a coverageData >= 15X There is a 0.44% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 76978754 0.3088407711529834 2.7305111015124988 chr2 243199373 76182805 0.31325247290008434 2.278764316175105 chr3 198022430 60266335 0.3043409526890464 1.970159332362299 chr4 191154276 53324460 0.27896033045057284 1.9469144022787574 chr5 180915260 52609430 0.2907959781833771 1.9145831720842268 chr6 171115067 50585861 0.29562482069448626 2.336234677038593 chr7 159138663 49357231 0.3101523543653248 2.4756794702346365 chr8 146364022 44434281 0.30358745539255544 2.1926461178062158 chr9 141213431 37903696 0.26841424170198086 1.8964699832457221 chr10 135534747 42710221 0.31512377412708786 2.088274387713686 chr11 135006516 41422689 0.3068199241583273 3.007107415786 chr12 133851895 41496444 0.3100176056528748 2.005669150298153 chr13 115169878 27043938 0.23481780539873456 1.7524991257037743 chr14 107349540 27218771 0.2535527492712125 1.8214029740506275 chr15 102531392 28162522 0.27467219015226085 1.8908129263100588 chr16 90354753 29713978 0.32885904740395894 2.0624326209867547 chr17 81195210 28977575 0.35688774005264595 2.3234510548582894 chr18 78077248 22472804 0.287827818931323 2.2592436130746045 chr19 59128983 22457429 0.37980408017503026 2.708486258510327 chr20 63025520 21452754 0.3403820230281321 2.1204043668917376 chr21 48129895 11990224 0.24912217240448997 1.8475144281676799 chr22 51304566 13196150 0.2572119994154127 1.8318262592097858 chrMT 16571 277446 16.742864039587232 22.94179911059471 chrX 155270560 26660564 0.17170392120695643 1.545002176069698 chrY 59373566 5705142 0.09608892280446824 1.047099573753235