BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472547.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 11,932,376 number of mapped reads = 11,783,081 (98.75%) number of supplementary alignments = 54,984 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,907,350 number of mapped paired reads (second in pair) = 5,875,731 number of mapped paired reads (both in pair) = 11,712,784 number of mapped paired reads (singletons) = 70,297 number of mapped bases = 1,155,558,068 bp number of sequenced bases = 1,155,359,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,443,982 duplication rate = 35.76% >>>>>>> Insert size mean insert size = 26,783.8946 std insert size = 1,520,492.0546 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 49.5256 >>>>>>> ACTG content number of A's = 326,476,683 bp (28.26%) number of C's = 251,945,608 bp (21.81%) number of T's = 323,193,535 bp (27.97%) number of G's = 253,561,999 bp (21.95%) number of N's = 181,468 bp (0.02%) GC percentage = 43.75% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 6,746,001 number of insertions = 49,738 mapped reads with insertion percentage = 0.42% number of deletions = 56,731 mapped reads with deletion percentage = 0.48% homopolymer indels = 49.25% >>>>>>> Coverage mean coverageData = 0.3733X std coverageData = 70.2926X There is a 1.58% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 39797520 0.1596686894513294 25.402631390211315 chr2 243199373 182015739 0.7484219089660236 121.81389743205597 chr3 198022430 18415788 0.09299849517047135 14.051546823273993 chr4 191154276 16073650 0.08408731594369356 3.3812487710336585 chr5 180915260 67336031 0.3721965244943959 59.228564537813085 chr6 171115067 92795410 0.5422983003594886 57.33152120710193 chr7 159138663 20113428 0.126389323755975 17.514732049481292 chr8 146364022 63174947 0.431628935422395 60.74045325231422 chr9 141213431 113348670 0.8026762695115027 98.82709983223008 chr10 135534747 7855996 0.057962966500391226 3.5110566478674907 chr11 135006516 26673168 0.1975694862016882 8.579546580048781 chr12 133851895 60993806 0.4556813035781077 66.35814993782117 chr13 115169878 48713790 0.4229733576690947 44.557556236638106 chr14 107349540 60465234 0.5632556413376341 49.453793156783064 chr15 102531392 2220566 0.021657425659450717 1.2749047045101336 chr16 90354753 6012327 0.06654134730466255 1.392696718761605 chr17 81195210 60438199 0.7443567052785502 75.13279796930954 chr18 78077248 18918241 0.24230158573212007 24.917044923575247 chr19 59128983 11284342 0.19084282237697206 10.513765291242294 chr20 63025520 1614447 0.025615766438737832 0.47632101581355224 chr21 48129895 4959419 0.1030423814554343 1.7940723257300302 chr22 51304566 894911 0.01744310633092579 1.518836062036163 chrMT 16571 2608 0.1573833806046708 0.7915866260122035 chrX 155270560 222108274 1.4304596698820433 207.29920331292982 chrY 59373566 9331557 0.15716686109101144 26.282748974184656