BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090198.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 25,537,121 number of mapped reads = 23,113,491 (90.51%) number of supplementary alignments = 157,619 (0.62%) number of secondary alignments = 0 number of mapped bases = 1,506,405,852 bp number of sequenced bases = 1,505,885,074 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,967,071 duplication rate = 11.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2844 >>>>>>> ACTG content number of A's = 405,119,783 bp (26.9%) number of C's = 280,792,511 bp (18.65%) number of T's = 469,109,773 bp (31.15%) number of G's = 349,935,830 bp (23.24%) number of N's = 927,177 bp (0.06%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 11,980,608 number of insertions = 99,238 mapped reads with insertion percentage = 0.43% number of deletions = 299,392 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.4866X std coverageData = 3.476X There is a 20.68% of reference with a coverageData >= 1X There is a 10.98% of reference with a coverageData >= 2X There is a 6.15% of reference with a coverageData >= 3X There is a 3.57% of reference with a coverageData >= 4X There is a 2.14% of reference with a coverageData >= 5X There is a 1.32% of reference with a coverageData >= 6X There is a 0.84% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 124197882 0.49828514569678845 6.512027772596808 chr2 243199373 178115015 0.732382706430744 4.186441642628684 chr3 198022430 141424366 0.7141835700127506 1.7177461448756113 chr4 191154276 57342362 0.29997948881875913 1.3133602450495068 chr5 180915260 69017437 0.3814904115882762 1.2192493938490658 chr6 171115067 84583431 0.49430732478981526 1.912352146207225 chr7 159138663 112635336 0.7077810877423295 7.059899165077211 chr8 146364022 137098584 0.9366959320098487 5.6437470804725605 chr9 141213431 47807034 0.33854452555578796 2.8231167851249226 chr10 135534747 46040210 0.3396930382730563 3.055667751916432 chr11 135006516 63218265 0.4682608430544197 2.3620509663127653 chr12 133851895 54921805 0.4103177246762177 1.3027141289882755 chr13 115169878 46113131 0.4003922883377544 1.181245147718921 chr14 107349540 44801658 0.41734373524097074 1.3914333703378892 chr15 102531392 40393205 0.3939593934314283 1.2086452158267988 chr16 90354753 30029270 0.33234853732597774 1.3044829688081687 chr17 81195210 30382195 0.3741870364027632 1.58207595938139 chr18 78077248 48430606 0.6202908944741495 4.630508710662925 chr19 59128983 25183955 0.425915578490501 3.830723005916981 chr20 63025520 37393582 0.5933085835705917 1.6168063874694185 chr21 48129895 22839672 0.47454231927994023 1.5507935395424175 chr22 51304566 12102512 0.23589541718372592 0.8882816352360609 chrMT 16571 2035304 122.82324542876108 60.49293592111481 chrX 155270560 46837243 0.3016492179844009 1.4758842249533692 chrY 59373566 3461792 0.05830527342757213 2.2789921498055796