BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472664.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 = 18,231,644 number of mapped reads = 18,106,771 (99.32%) number of supplementary alignments = 113,441 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,071,975 number of mapped paired reads (second in pair) = 9,034,796 number of mapped paired reads (both in pair) = 18,025,988 number of mapped paired reads (singletons) = 80,783 number of mapped bases = 1,781,698,236 bp number of sequenced bases = 1,781,459,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,060,393 duplication rate = 50.14% >>>>>>> Insert size mean insert size = 22,093.2858 std insert size = 1,462,872.6024 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.7264 >>>>>>> ACTG content number of A's = 483,175,600 bp (27.12%) number of C's = 409,508,205 bp (22.99%) number of T's = 483,488,106 bp (27.14%) number of G's = 404,944,479 bp (22.73%) number of N's = 343,583 bp (0.02%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,114,587 number of insertions = 115,098 mapped reads with insertion percentage = 0.63% number of deletions = 98,625 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.5755X std coverageData = 29.3985X There is a 3.41% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 213423532 0.8562607833984093 34.83473281330526 chr2 243199373 129920079 0.5342122284172172 24.984124848253515 chr3 198022430 153974638 0.7775616024911925 23.812164110092503 chr4 191154276 39193667 0.2050368310882044 11.351944534516134 chr5 180915260 77726221 0.429627777115098 21.734864287574393 chr6 171115067 146112244 0.853882983898782 32.16329159965639 chr7 159138663 97059107 0.6099027424906793 43.54825312382001 chr8 146364022 108151344 0.7389202791926557 38.36889553821572 chr9 141213431 157909197 1.1182307226852948 54.01489403224863 chr10 135534747 30907991 0.22804477585367833 12.169455856149332 chr11 135006516 35322657 0.2616366827805556 12.51703036566148 chr12 133851895 50110585 0.3743733699100786 15.234982587871723 chr13 115169878 48379617 0.42007179168844827 19.331396398949014 chr14 107349540 24958904 0.2325012664236847 12.66171260702642 chr15 102531392 14891839 0.1452417519114536 5.627957794135922 chr16 90354753 118165247 1.3077922641214015 62.543637701063474 chr17 81195210 58593447 0.7216367443350414 33.9581562000749 chr18 78077248 22214563 0.28452031249871923 22.647964553325284 chr19 59128983 34545662 0.5842424517939029 22.87473634632091 chr20 63025520 58275679 0.9246362267221278 31.742333974793407 chr21 48129895 15058632 0.31287481512270077 23.203656561130238 chr22 51304566 26266190 0.5119659330126679 21.53300109881144 chrMT 16571 5624 0.33938808762295575 0.8613101254317009 chrX 155270560 119774020 0.7713891158761841 28.395805173353224 chrY 59373566 757550 0.01275904499318771 0.9218929678059418