BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472527.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,221,100 number of mapped reads = 16,076,893 (99.11%) number of supplementary alignments = 68,316 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,059,295 number of mapped paired reads (second in pair) = 8,017,598 number of mapped paired reads (both in pair) = 15,997,776 number of mapped paired reads (singletons) = 79,117 number of mapped bases = 1,581,710,028 bp number of sequenced bases = 1,581,507,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,494,566 duplication rate = 46.09% >>>>>>> Insert size mean insert size = 30,408.6506 std insert size = 1,744,929.6677 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.982 >>>>>>> ACTG content number of A's = 434,108,461 bp (27.45%) number of C's = 358,415,052 bp (22.66%) number of T's = 432,153,368 bp (27.33%) number of G's = 356,583,109 bp (22.55%) number of N's = 247,092 bp (0.02%) GC percentage = 45.21% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 8,740,521 number of insertions = 80,937 mapped reads with insertion percentage = 0.5% number of deletions = 81,159 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.48% >>>>>>> Coverage mean coverageData = 0.5109X std coverageData = 20.5364X There is a 4.91% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 114900742 0.46098477724555 17.236574590605887 chr2 243199373 114898243 0.4724446514095248 17.04833272172747 chr3 198022430 190325002 0.9611285044830528 26.593029898932773 chr4 191154276 109192974 0.5712295653799552 27.58696543974652 chr5 180915260 101954321 0.5635473812435723 24.178920894417633 chr6 171115067 41961019 0.24522106519117923 11.775621165490861 chr7 159138663 66041795 0.41499528621778103 13.8129977657645 chr8 146364022 77665007 0.5306290845164121 17.959521627736027 chr9 141213431 131968354 0.9345311778452575 32.167473971367656 chr10 135534747 35205076 0.25974945008013334 23.355985819149353 chr11 135006516 68498518 0.5073719404773026 24.192070711451947 chr12 133851895 75753716 0.5659517633276689 17.354739056039406 chr13 115169878 41256320 0.358221443978607 13.21535791630656 chr14 107349540 79601199 0.7415141136142736 35.26476706278481 chr15 102531392 48991153 0.4778161306929296 17.811391231642133 chr16 90354753 40130906 0.4441482563734085 12.952846283828773 chr17 81195210 41132322 0.5065855732130011 16.29563881089269 chr18 78077248 30349390 0.38870978136934337 13.795671515182702 chr19 59128983 30632382 0.518060356289233 19.023483897484397 chr20 63025520 33917181 0.5381499589372686 14.838359044988552 chr21 48129895 4269400 0.08870578254949445 3.250015434325037 chr22 51304566 17757818 0.3461254891036404 15.524869355157223 chrMT 16571 1514 0.09136443183875445 0.436939715130021 chrX 155270560 80807147 0.5204280000020609 16.490080104067168 chrY 59373566 4498529 0.07576652882867099 3.352663638321588