BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238655.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 = 3,595,423 number of mapped reads = 2,847,351 (79.19%) number of supplementary alignments = 24,678 (0.69%) number of secondary alignments = 0 number of mapped bases = 170,854,242 bp number of sequenced bases = 170,773,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,429,986 duplication rate = 23.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2785 >>>>>>> ACTG content number of A's = 43,117,773 bp (25.25%) number of C's = 28,796,406 bp (16.86%) number of T's = 58,313,093 bp (34.15%) number of G's = 40,542,670 bp (23.74%) number of N's = 3,842 bp (0%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 996,171 number of insertions = 11,091 mapped reads with insertion percentage = 0.39% number of deletions = 47,473 mapped reads with deletion percentage = 1.65% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.0552X std coverageData = 1.1925X There is a 1.02% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 28372960 0.11383305640791162 1.4103272263824065 chr2 243199373 16427917 0.06754917497258514 1.6779030427239479 chr3 198022430 10059181 0.05079818988182298 0.879047476800254 chr4 191154276 11439578 0.059844740276696715 0.9390839477897264 chr5 180915260 6993722 0.03865744658576618 0.7600389627798484 chr6 171115067 7884136 0.04607505427911851 1.0623742190001708 chr7 159138663 6104263 0.03835813927882503 0.82068027900211 chr8 146364022 13036330 0.08906785849325731 1.8179037659695345 chr9 141213431 5083267 0.03599705045053399 0.7448582102509986 chr10 135534747 5100527 0.037632615346970766 0.8454806527677631 chr11 135006516 8461985 0.06267834509558043 0.9626956798447989 chr12 133851895 5259248 0.03929154682494409 0.7534214305762132 chr13 115169878 5222686 0.045347673286586274 1.000527758774888 chr14 107349540 2906006 0.02707050258436133 0.7339496103712714 chr15 102531392 4185917 0.04082571121242556 0.897113059038523 chr16 90354753 3378955 0.037396538508605075 0.7518319494630067 chr17 81195210 3717319 0.04578249135632508 0.7986747892301432 chr18 78077248 7725705 0.09894950447023952 3.544729915991292 chr19 59128983 2576444 0.04357328452613501 0.8711059246151247 chr20 63025520 4895421 0.07767363125286392 1.0723651493347313 chr21 48129895 1676225 0.034827106936343825 0.7081593293551363 chr22 51304566 1136877 0.022159372715481112 0.5638840818605301 chrMT 16571 43920 2.6504133727596404 6.420118346895521 chrX 155270560 8677140 0.05588400016075166 0.9059141373862102 chrY 59373566 488513 0.008227786082446184 0.3705599079737392