BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975207.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,808,684 number of mapped reads = 2,786,463 (99.21%) number of supplementary alignments = 126,018 (4.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,394,919 number of mapped paired reads (second in pair) = 1,391,544 number of mapped paired reads (both in pair) = 2,778,910 number of mapped paired reads (singletons) = 7,553 number of mapped bases = 394,239,567 bp number of sequenced bases = 394,082,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 417,674 duplication rate = 14.5% >>>>>>> Insert size mean insert size = 216,632.9424 std insert size = 4,412,478.0338 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.9103 >>>>>>> ACTG content number of A's = 115,533,813 bp (29.32%) number of C's = 81,680,129 bp (20.73%) number of T's = 114,277,527 bp (29%) number of G's = 82,568,392 bp (20.95%) number of N's = 22,695 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 3,147,670 number of insertions = 58,764 mapped reads with insertion percentage = 2% number of deletions = 58,678 mapped reads with deletion percentage = 2.01% homopolymer indels = 41.69% >>>>>>> Coverage mean coverageData = 0.1274X std coverageData = 1.5782X There is a 7.64% of reference with a coverageData >= 1X There is a 4.18% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 32552624 0.13060197751723956 4.139434915284626 chr2 243199373 33506196 0.13777254269483663 0.9670146950989154 chr3 198022430 25642284 0.1294918156493686 0.5053519129030387 chr4 191154276 25712432 0.13451141422543955 1.0653818010639022 chr5 180915260 23277291 0.12866405520463006 0.4755021740697592 chr6 171115067 22624340 0.13221711212607595 0.5538354165848277 chr7 159138663 21142763 0.1328574879380506 1.0526052043825345 chr8 146364022 19708618 0.13465479925114385 1.213491160527951 chr9 141213431 16746259 0.11858828782369858 1.6109599142871167 chr10 135534747 20823610 0.1536403797618038 2.967845914642049 chr11 135006516 17325570 0.1283313614285106 0.6654823573690013 chr12 133851895 17315696 0.1293645936054921 0.47634889436574385 chr13 115169878 12596245 0.10937100237268638 0.4403723180233462 chr14 107349540 11858128 0.11046277422334554 0.44379299693604607 chr15 102531392 11494908 0.11211110837157073 0.442090275184328 chr16 90354753 12473143 0.1380463405173605 0.983022624660189 chr17 81195210 10948458 0.1348411809021739 0.6970854920575702 chr18 78077248 10944539 0.14017577822415053 1.6026027993755987 chr19 59128983 7822465 0.13229493563249684 1.969284438837998 chr20 63025520 8275535 0.13130450966529114 0.6198526612254278 chr21 48129895 5331039 0.1107635701262178 0.677485179883899 chr22 51304566 4787510 0.09331547605333997 0.4103542069718104 chrMT 16571 270552 16.326836038863075 6.5809183614217375 chrX 155270560 19800384 0.12752181740054264 0.5468095267108088 chrY 59373566 1258978 0.021204352118584218 1.1709583791108922