BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472659.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 = 42,099,560 number of mapped reads = 41,768,002 (99.21%) number of supplementary alignments = 265,631 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,944,128 number of mapped paired reads (second in pair) = 20,823,874 number of mapped paired reads (both in pair) = 41,542,282 number of mapped paired reads (singletons) = 225,720 number of mapped bases = 4,114,557,090 bp number of sequenced bases = 4,113,951,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,975,059 duplication rate = 50.94% >>>>>>> Insert size mean insert size = 22,773.7655 std insert size = 1,494,483.9065 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 54.9795 >>>>>>> ACTG content number of A's = 1,108,173,400 bp (26.94%) number of C's = 953,430,897 bp (23.18%) number of T's = 1,110,623,029 bp (27%) number of G's = 940,931,223 bp (22.87%) number of N's = 792,803 bp (0.02%) GC percentage = 46.05% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 25,792,671 number of insertions = 297,620 mapped reads with insertion percentage = 0.71% number of deletions = 233,158 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 1.3291X std coverageData = 51.8603X There is a 7.68% of reference with a coverageData >= 1X There is a 3.54% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.39% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.36% of reference with a coverageData >= 21X There is a 0.35% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.3% of reference with a coverageData >= 34X There is a 0.29% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.26% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.26% of reference with a coverageData >= 49X There is a 0.25% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 483103693 1.9382246313440479 78.73775768805855 chr2 243199373 285001156 1.1718827745497518 49.399467548844626 chr3 198022430 374895852 1.8931989270104401 53.65703149273847 chr4 191154276 115722506 0.6053880060731678 31.37927072249442 chr5 180915260 152122993 0.8408521923468479 27.86142605207924 chr6 171115067 385942744 2.2554573993183196 66.50751214718571 chr7 159138663 290768993 1.8271423645176659 77.77950368707013 chr8 146364022 198242978 1.3544515605071306 45.39280399788131 chr9 141213431 266830809 1.8895568722496374 45.62583021077558 chr10 135534747 101574600 0.7494358623770478 46.95110204209808 chr11 135006516 104997193 0.7777194472598641 33.16124134338128 chr12 133851895 148651009 1.1105633506346697 29.913362216065213 chr13 115169878 119304315 1.035898596679941 39.01319179106751 chr14 107349540 53090529 0.49455758264078264 21.394603294093635 chr15 102531392 34448847 0.33598341276786725 16.111033347007925 chr16 90354753 226736459 2.5094026763594828 89.09392869466052 chr17 81195210 186067227 2.291603494836703 64.94588884049216 chr18 78077248 27794936 0.3559927726960868 14.192802171605488 chr19 59128983 129277311 2.186361145430152 61.50514208411195 chr20 63025520 184712875 2.930763205127066 82.10274368620053 chr21 48129895 35612185 0.7399181942948349 42.69121481565641 chr22 51304566 77232074 1.505364532271845 68.49373984818494 chrMT 16571 62130 3.7493211031319778 2.7801341561922976 chrX 155270560 129407651 0.833433272862544 25.508879526088304 chrY 59373566 2956025 0.0497868866424496 2.1122198817050575