BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238674.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,345,499 number of mapped reads = 3,024,227 (90.4%) number of supplementary alignments = 32,027 (0.96%) number of secondary alignments = 0 number of mapped bases = 187,249,257 bp number of sequenced bases = 187,153,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 681,003 duplication rate = 17.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.463 >>>>>>> ACTG content number of A's = 47,776,279 bp (25.53%) number of C's = 33,429,102 bp (17.86%) number of T's = 62,120,195 bp (33.19%) number of G's = 43,818,588 bp (23.41%) number of N's = 9,480 bp (0.01%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,177,232 number of insertions = 13,409 mapped reads with insertion percentage = 0.44% number of deletions = 56,247 mapped reads with deletion percentage = 1.84% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 0.8923X There is a 3.29% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 8518216 0.03417530502361316 1.3869369971451861 chr2 243199373 12262052 0.05041975169894866 1.8431113897460019 chr3 198022430 3970707 0.02005180423248013 0.2536823732646518 chr4 191154276 18300908 0.0957389412518295 0.5166610201619705 chr5 180915260 11844237 0.06546842427775303 0.4418927715596075 chr6 171115067 8021199 0.04687605329342506 0.6360116210080413 chr7 159138663 9783154 0.06147565786700118 0.555309024549193 chr8 146364022 7865063 0.05373631369599832 1.1207203987048977 chr9 141213431 15592325 0.11041672799522873 0.8464554624858186 chr10 135534747 14547207 0.10733193754366177 0.6181814713464443 chr11 135006516 15363123 0.11379541858557404 0.6373675973044898 chr12 133851895 1713172 0.012799011922842034 0.25431446873105457 chr13 115169878 684037 0.005939374182544502 0.4110861201172784 chr14 107349540 1032625 0.009619277362529918 0.3940274115163058 chr15 102531392 3182919 0.031043360846988208 0.4321860252122434 chr16 90354753 3116819 0.03449535189366297 0.4432236233737192 chr17 81195210 8821379 0.10864408134420737 0.600438375713855 chr18 78077248 11251211 0.14410358059751285 1.92731752458821 chr19 59128983 9422382 0.1593530198210918 0.9307120400284122 chr20 63025520 7225017 0.11463637269474333 0.5919635243808015 chr21 48129895 6216603 0.1291630285085808 0.6342342922754801 chr22 51304566 2395014 0.046682277752822236 0.3522854253200368 chrMT 16571 476411 28.749683181461588 17.877417368199687 chrX 155270560 5210585 0.03355810013179575 0.3635550907937814 chrY 59373566 432892 0.007290988720468634 0.3106052540617096