BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714090.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 19,422 number of mapped reads = 6,669 (34.34%) number of supplementary alignments = 147 (0.76%) number of secondary alignments = 0 number of mapped bases = 780,627 bp number of sequenced bases = 766,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,214 duplication rate = 42.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 19.59 >>>>>>> ACTG content number of A's = 168,373 bp (21.98%) number of C's = 137,816 bp (17.99%) number of T's = 154,274 bp (20.14%) number of G's = 305,701 bp (39.9%) number of N's = 12 bp (0%) GC percentage = 57.89% >>>>>>> Mismatches and indels general error rate = 0.0371 number of mismatches = 27,198 number of insertions = 419 mapped reads with insertion percentage = 5.37% number of deletions = 1,925 mapped reads with deletion percentage = 28.04% homopolymer indels = 30.08% >>>>>>> Coverage mean coverageData = 0.0003X std coverageData = 0.2385X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 7638 3.0643855447004084E-5 0.014449947010484526 chr2 243199373 180471 7.420701697286037E-4 0.7757588680091871 chr3 198022430 7176 3.6238319063148556E-5 0.02307353193464752 chr4 191154276 11789 6.167269833921999E-5 0.03896052563342991 chr5 180915260 6439 3.559124863209438E-5 0.027226350770658405 chr6 171115067 15040 8.789407188789518E-5 0.04324765368054021 chr7 159138663 17184 1.0798130181601438E-4 0.05891119088729012 chr8 146364022 14299 9.769477365141004E-5 0.055969492512271346 chr9 141213431 6254 4.4287572051131594E-5 0.021381398154070017 chr10 135534747 5502 4.05947561181488E-5 0.01922539326500852 chr11 135006516 15890 1.1769802281246929E-4 0.05857447719325931 chr12 133851895 7381 5.51430370111682E-5 0.023213226382030605 chr13 115169878 3149 2.7342218770085005E-5 0.009742240155425465 chr14 107349540 599 5.579902810948235E-6 0.0033973084044838908 chr15 102531392 4270 4.16457820059636E-5 0.016251238514454987 chr16 90354753 7104 7.86234233853752E-5 0.043711886290175306 chr17 81195210 4944 6.089029143467946E-5 0.02866393655462292 chr18 78077248 2743 3.513187350045944E-5 0.011582778984440592 chr19 59128983 5467 9.24588877167057E-5 0.05386082446939384 chr20 63025520 17494 2.775701017619529E-4 0.1423328395088583 chr21 48129895 919 1.909416174708048E-5 0.0056326084978470334 chr22 51304566 1145 2.2317701703197335E-5 0.012556503517707556 chrMT 16571 602 0.036328525737734596 0.33449971989484967 chrX 155270560 434399 0.0027976906890784703 0.4043032141482244 chrY 59373566 2729 4.596321534738203E-5 0.011553129777580442