BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472675.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 = 17,029,742 number of mapped reads = 16,888,744 (99.17%) number of supplementary alignments = 99,753 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,468,040 number of mapped paired reads (second in pair) = 8,420,704 number of mapped paired reads (both in pair) = 16,800,696 number of mapped paired reads (singletons) = 88,048 number of mapped bases = 1,660,242,294 bp number of sequenced bases = 1,660,033,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,736,916 duplication rate = 49.15% >>>>>>> Insert size mean insert size = 24,875.96 std insert size = 1,611,554.0034 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.8354 >>>>>>> ACTG content number of A's = 439,555,600 bp (26.48%) number of C's = 392,251,478 bp (23.63%) number of T's = 439,896,219 bp (26.5%) number of G's = 388,018,026 bp (23.37%) number of N's = 312,607 bp (0.02%) GC percentage = 47% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,969,484 number of insertions = 99,951 mapped reads with insertion percentage = 0.58% number of deletions = 86,569 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.5363X std coverageData = 24.6795X There is a 3.4% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188075397 0.7545634038761332 30.074246383793543 chr2 243199373 116138945 0.4775462352857299 24.200064480535136 chr3 198022430 168407229 0.8504452197662659 28.826152028681257 chr4 191154276 43758140 0.22891530817756858 12.86483606164119 chr5 180915260 45649081 0.25232299917652057 10.325589597719762 chr6 171115067 152609740 0.891854485262832 41.830989921659565 chr7 159138663 89281592 0.5610301753006434 20.22407003329992 chr8 146364022 74517524 0.5091245989400318 19.116214569819824 chr9 141213431 92943210 0.6581754252539902 18.203788692429576 chr10 135534747 36281025 0.2676879973812177 22.794436856853363 chr11 135006516 40312117 0.29859386194367094 14.960525327624499 chr12 133851895 86953772 0.6496267535099148 27.37861617049485 chr13 115169878 37430532 0.32500279283095185 12.319184014029188 chr14 107349540 21234289 0.197805123338209 8.2852291339674 chr15 102531392 31304417 0.30531543939245454 24.40128390121341 chr16 90354753 84619288 0.9365228191150055 30.94489439257871 chr17 81195210 51094997 0.6292858531925714 23.015371550711556 chr18 78077248 11643205 0.14912417251181803 7.1449389005254424 chr19 59128983 67449620 1.1407201101361746 42.03627857191822 chr20 63025520 83770654 1.3291545075709015 50.07444731387235 chr21 48129895 6546033 0.13600763101602445 9.981104210304768 chr22 51304566 25913779 0.5050969342572745 20.485001353075194 chrMT 16571 8655 0.5222979904652707 0.8885975837419979 chrX 155270560 102592880 0.6607362013764876 28.682205110114978 chrY 59373566 1706173 0.028736239288709726 1.755826174372812