BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046534.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,777,684 number of mapped reads = 9,591,304 (98.09%) number of supplementary alignments = 57,587 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,871,441 number of mapped paired reads (second in pair) = 4,719,863 number of mapped paired reads (both in pair) = 9,425,136 number of mapped paired reads (singletons) = 166,168 number of mapped bases = 917,883,180 bp number of sequenced bases = 917,631,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,937,707 duplication rate = 35.56% >>>>>>> Insert size mean insert size = 28,959.6626 std insert size = 1,680,836.2124 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 51.925 >>>>>>> ACTG content number of A's = 272,792,028 bp (29.73%) number of C's = 186,961,762 bp (20.37%) number of T's = 270,613,619 bp (29.49%) number of G's = 187,180,801 bp (20.4%) number of N's = 83,369 bp (0.01%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 3,946,271 number of insertions = 79,421 mapped reads with insertion percentage = 0.81% number of deletions = 94,244 mapped reads with deletion percentage = 0.95% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.2965X std coverageData = 26.8226X There is a 3.56% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 92488455 0.37106609656150064 28.07879277073705 chr2 243199373 127582566 0.5246007192625451 31.951388353329705 chr3 198022430 36745521 0.18556241835836476 9.826916527135237 chr4 191154276 27231996 0.14246082572591784 13.30777142569695 chr5 180915260 55949412 0.3092575606944378 15.271149403018152 chr6 171115067 114047721 0.6664972465574875 65.18401682488602 chr7 159138663 67211091 0.4223429412624888 34.22380262870364 chr8 146364022 121164894 0.8278324983444361 49.840494413748665 chr9 141213431 17510399 0.12399952947818399 11.038777909214241 chr10 135534747 38083705 0.2809884981007859 29.347054830464646 chr11 135006516 8861966 0.06564102431915213 4.567581971769737 chr12 133851895 37662882 0.28137727896941617 16.016488193748415 chr13 115169878 54647387 0.4744937474015558 30.5064532194291 chr14 107349540 28207456 0.26276270955609127 13.84952563669051 chr15 102531392 6564382 0.06402314327303778 3.8107091819053367 chr16 90354753 31551447 0.3491952105718224 28.72315627258625 chr17 81195210 22083696 0.271982743809641 13.60293389764747 chr18 78077248 2457850 0.031479721211485324 1.3865324529271215 chr19 59128983 1783394 0.030161080226933718 1.5605750080064906 chr20 63025520 6103580 0.09684299312405514 5.9375433954951715 chr21 48129895 6597540 0.13707779748948132 17.522246653331006 chr22 51304566 6875677 0.1340168631384583 7.290741043955834 chrMT 16571 67582 4.078329611972723 2.9826842030014364 chrX 155270560 6118451 0.039405093921217264 0.6969799432281971 chrY 59373566 284130 0.004785462944907166 0.8733089120467121