BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 49,841,482 number of mapped reads = 48,350,943 (97.01%) number of supplementary alignments = 1,320,457 (2.65%) number of secondary alignments = 0 number of mapped bases = 4,560,192,196 bp number of sequenced bases = 4,557,637,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,693,329 duplication rate = 38.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7471 >>>>>>> ACTG content number of A's = 1,189,416,421 bp (26.1%) number of C's = 1,070,532,624 bp (23.49%) number of T's = 1,201,052,323 bp (26.35%) number of G's = 1,071,376,813 bp (23.51%) number of N's = 25,259,484 bp (0.55%) GC percentage = 47% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 40,992,233 number of insertions = 1,600,543 mapped reads with insertion percentage = 3.14% number of deletions = 1,227,624 mapped reads with deletion percentage = 2.46% homopolymer indels = 43.14% >>>>>>> Coverage mean coverageData = 1.4731X std coverageData = 59.392X There is a 7.09% of reference with a coverageData >= 1X There is a 4.71% of reference with a coverageData >= 2X There is a 3.74% of reference with a coverageData >= 3X There is a 3.23% of reference with a coverageData >= 4X There is a 2.89% of reference with a coverageData >= 5X There is a 2.64% of reference with a coverageData >= 6X There is a 2.45% of reference with a coverageData >= 7X There is a 2.29% of reference with a coverageData >= 8X There is a 2.15% of reference with a coverageData >= 9X There is a 2.04% of reference with a coverageData >= 10X There is a 1.94% of reference with a coverageData >= 11X There is a 1.85% of reference with a coverageData >= 12X There is a 1.77% of reference with a coverageData >= 13X There is a 1.7% of reference with a coverageData >= 14X There is a 1.64% of reference with a coverageData >= 15X There is a 1.58% of reference with a coverageData >= 16X There is a 1.52% of reference with a coverageData >= 17X There is a 1.47% of reference with a coverageData >= 18X There is a 1.42% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.34% of reference with a coverageData >= 21X There is a 1.3% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.22% of reference with a coverageData >= 24X There is a 1.19% of reference with a coverageData >= 25X There is a 1.16% of reference with a coverageData >= 26X There is a 1.13% of reference with a coverageData >= 27X There is a 1.1% of reference with a coverageData >= 28X There is a 1.07% of reference with a coverageData >= 29X There is a 1.05% of reference with a coverageData >= 30X There is a 1.02% of reference with a coverageData >= 31X There is a 1% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.95% of reference with a coverageData >= 34X There is a 0.93% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.89% of reference with a coverageData >= 37X There is a 0.87% of reference with a coverageData >= 38X There is a 0.85% of reference with a coverageData >= 39X There is a 0.84% of reference with a coverageData >= 40X There is a 0.82% of reference with a coverageData >= 41X There is a 0.8% of reference with a coverageData >= 42X There is a 0.79% of reference with a coverageData >= 43X There is a 0.77% of reference with a coverageData >= 44X There is a 0.76% of reference with a coverageData >= 45X There is a 0.74% of reference with a coverageData >= 46X There is a 0.73% of reference with a coverageData >= 47X There is a 0.71% of reference with a coverageData >= 48X There is a 0.7% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 329860193 1.3234077077785897 14.40599026265432 chr2 243199373 230990627 0.9497994347214045 25.692394407713397 chr3 198022430 220840896 1.115231724002175 21.700996099016695 chr4 191154276 241413057 1.2629226091704064 15.796326497350028 chr5 180915260 209445521 1.1576995826664926 16.25356665490512 chr6 171115067 57464300 0.3358225608502377 8.766251395112564 chr7 159138663 257858772 1.6203401935078467 20.691379880455084 chr8 146364022 106220029 0.725724994083587 9.287440067162336 chr9 141213431 50093176 0.3547337929916879 20.507355637517684 chr10 135534747 416202238 3.0708157665281215 268.50070099625947 chr11 135006516 447925716 3.3178081271277304 36.46875146381502 chr12 133851895 102663299 0.7669917486039327 11.356419913029915 chr13 115169878 136224350 1.1828123148658714 14.047102906873262 chr14 107349540 69880866 0.6509656771701118 8.795689838520426 chr15 102531392 291166176 2.8397759000482505 21.030733079850286 chr16 90354753 319305223 3.533906212991363 30.118161256306383 chr17 81195210 173305783 2.134433582966286 23.617747526254703 chr18 78077248 127832191 1.637252775610124 16.346031625621116 chr19 59128983 312853248 5.291030424115362 30.441360872144212 chr20 63025520 167271544 2.6540287807224754 23.879002682037058 chr21 48129895 112353776 2.334386476430086 30.294743910630494 chr22 51304566 81960220 1.5975229183305049 18.24465500658016 chrMT 16571 2526755 152.48053828978337 94.52920501229832 chrX 155270560 79895672 0.5145577629139741 6.591238081058663 chrY 59373566 14638568 0.24655025773590894 13.288005203288824