BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514705.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 = 102,816,684 number of mapped reads = 102,090,922 (99.29%) number of supplementary alignments = 4,596,038 (4.47%) number of secondary alignments = 0 number of mapped bases = 9,818,146,150 bp number of sequenced bases = 9,812,288,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,760,786 duplication rate = 43.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5149 >>>>>>> ACTG content number of A's = 2,884,216,055 bp (29.39%) number of C's = 2,030,163,941 bp (20.69%) number of T's = 2,833,505,900 bp (28.88%) number of G's = 2,059,714,988 bp (20.99%) number of N's = 4,687,933 bp (0.05%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 56,193,101 number of insertions = 2,986,762 mapped reads with insertion percentage = 2.84% number of deletions = 2,965,312 mapped reads with deletion percentage = 2.82% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 3.1715X std coverageData = 74.5857X There is a 10.94% of reference with a coverageData >= 1X There is a 7.47% of reference with a coverageData >= 2X There is a 6.14% of reference with a coverageData >= 3X There is a 5.49% of reference with a coverageData >= 4X There is a 5.06% of reference with a coverageData >= 5X There is a 4.75% of reference with a coverageData >= 6X There is a 4.5% of reference with a coverageData >= 7X There is a 4.29% of reference with a coverageData >= 8X There is a 4.1% of reference with a coverageData >= 9X There is a 3.94% of reference with a coverageData >= 10X There is a 3.79% of reference with a coverageData >= 11X There is a 3.66% of reference with a coverageData >= 12X There is a 3.54% of reference with a coverageData >= 13X There is a 3.42% of reference with a coverageData >= 14X There is a 3.31% of reference with a coverageData >= 15X There is a 3.22% of reference with a coverageData >= 16X There is a 3.12% of reference with a coverageData >= 17X There is a 3.03% of reference with a coverageData >= 18X There is a 2.95% of reference with a coverageData >= 19X There is a 2.87% of reference with a coverageData >= 20X There is a 2.8% of reference with a coverageData >= 21X There is a 2.73% of reference with a coverageData >= 22X There is a 2.66% of reference with a coverageData >= 23X There is a 2.59% of reference with a coverageData >= 24X There is a 2.53% of reference with a coverageData >= 25X There is a 2.47% of reference with a coverageData >= 26X There is a 2.41% of reference with a coverageData >= 27X There is a 2.36% of reference with a coverageData >= 28X There is a 2.31% of reference with a coverageData >= 29X There is a 2.26% of reference with a coverageData >= 30X There is a 2.21% of reference with a coverageData >= 31X There is a 2.16% of reference with a coverageData >= 32X There is a 2.11% of reference with a coverageData >= 33X There is a 2.07% of reference with a coverageData >= 34X There is a 2.03% of reference with a coverageData >= 35X There is a 1.99% of reference with a coverageData >= 36X There is a 1.95% of reference with a coverageData >= 37X There is a 1.91% of reference with a coverageData >= 38X There is a 1.87% of reference with a coverageData >= 39X There is a 1.84% of reference with a coverageData >= 40X There is a 1.8% of reference with a coverageData >= 41X There is a 1.77% of reference with a coverageData >= 42X There is a 1.74% of reference with a coverageData >= 43X There is a 1.7% of reference with a coverageData >= 44X There is a 1.67% of reference with a coverageData >= 45X There is a 1.64% of reference with a coverageData >= 46X There is a 1.61% of reference with a coverageData >= 47X There is a 1.59% of reference with a coverageData >= 48X There is a 1.56% of reference with a coverageData >= 49X There is a 1.53% of reference with a coverageData >= 50X There is a 1.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 800724349 3.212526997074162 41.23404848013754 chr2 243199373 591487608 2.432109921599181 27.116002500209888 chr3 198022430 463235144 2.3393064310946996 25.173623612200693 chr4 191154276 759534686 3.973411957575043 29.51196249867156 chr5 180915260 877305165 4.849260172967167 45.933161636737026 chr6 171115067 430747104 2.517295008276507 26.705724328660867 chr7 159138663 419587738 2.636617212248415 26.207040846597803 chr8 146364022 530567658 3.6249868700656505 37.15578814236678 chr9 141213431 426020806 3.0168575537266 237.8657129945833 chr10 135534747 350266524 2.5843300832663965 24.650610041798824 chr11 135006516 495097699 3.667213358798178 34.59737321364743 chr12 133851895 474619896 3.5458586223228292 64.85215250018706 chr13 115169878 371853169 3.2287363280874537 27.368519886033056 chr14 107349540 358655916 3.3410102735419267 116.24345111330709 chr15 102531392 417665140 4.073534279140578 65.53687532587358 chr16 90354753 405138582 4.4838657463874645 52.64271273816511 chr17 81195210 266495089 3.28215283881894 37.82502451112027 chr18 78077248 283594459 3.632229186663956 29.949041789368952 chr19 59128983 447893766 7.574859963344879 262.6471641572811 chr20 63025520 192686586 3.0572787975410596 29.5185980626097 chr21 48129895 32520991 0.6756921244062551 10.31543341375228 chr22 51304566 118697496 2.313585422396907 33.63033356312228 chrMT 16571 3708290 223.78190815279706 104.26744211454654 chrX 155270560 213031000 1.371998658341929 22.219935459633657 chrY 59373566 87011289 1.4654886822866593 19.667569349703037