BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080632.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,984,156 number of mapped reads = 3,986,143 (79.98%) number of supplementary alignments = 34,833 (0.7%) number of secondary alignments = 0 number of mapped bases = 266,271,799 bp number of sequenced bases = 266,168,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,870 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1939 >>>>>>> ACTG content number of A's = 73,801,246 bp (27.73%) number of C's = 47,581,851 bp (17.88%) number of T's = 86,570,436 bp (32.52%) number of G's = 57,995,162 bp (21.79%) number of N's = 219,861 bp (0.08%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,394,647 number of insertions = 21,498 mapped reads with insertion percentage = 0.54% number of deletions = 63,423 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.086X std coverageData = 0.4907X There is a 6.8% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 31538217 0.12653215014457275 0.7223198647556475 chr2 243199373 24605556 0.1011744220245173 0.5422784409470944 chr3 198022430 15060435 0.07605418739685196 0.32982131996911096 chr4 191154276 18675431 0.09769821209754156 0.3828769774714656 chr5 180915260 17846648 0.09864644917183879 0.38095771234612263 chr6 171115067 18423706 0.10766851992057484 0.5609104140785353 chr7 159138663 9788697 0.06151048912607743 0.8348912331258426 chr8 146364022 24676187 0.1685946222494487 0.7536932158192748 chr9 141213431 10236034 0.07248626371807368 0.4099282702250369 chr10 135534747 14401801 0.10625910564469493 0.48668883862583445 chr11 135006516 12227216 0.09056759897425988 0.43991836023302305 chr12 133851895 8495171 0.06346694606004644 0.3057157572962305 chr13 115169878 4304745 0.03737735139391222 0.22616106638274988 chr14 107349540 4822286 0.04492134759031105 0.27935996247383615 chr15 102531392 4975654 0.0485281034709838 0.2628049516998098 chr16 90354753 3826642 0.04235130829254771 0.25457560209190233 chr17 81195210 6138359 0.07560001384318114 0.36419054066628775 chr18 78077248 6777891 0.08681006533426998 0.5788302723025383 chr19 59128983 3196339 0.054057060308309375 0.5028732171800191 chr20 63025520 5274816 0.08369333565197082 0.3515492005879731 chr21 48129895 3478971 0.07228295428444213 0.33234249370266156 chr22 51304566 2213073 0.04313598520646291 0.24442785242792284 chrMT 16571 98759 5.959748959024802 7.275538533777565 chrX 155270560 14732075 0.0948800274823508 0.3993412162288891 chrY 59373566 457090 0.007698543826725853 0.1291182448655511