BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124831.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 24,432,478 number of mapped reads = 24,224,832 (99.15%) number of supplementary alignments = 87,516 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,130,714 number of mapped paired reads (second in pair) = 12,094,118 number of mapped paired reads (both in pair) = 24,146,766 number of mapped paired reads (singletons) = 78,066 number of mapped bases = 2,146,725,668 bp number of sequenced bases = 2,145,729,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,846,078 duplication rate = 14.79% >>>>>>> Insert size mean insert size = 30,282.1926 std insert size = 1,616,103.8274 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 52.8328 >>>>>>> ACTG content number of A's = 611,309,957 bp (28.49%) number of C's = 396,377,043 bp (18.47%) number of T's = 638,990,871 bp (29.78%) number of G's = 499,031,040 bp (23.26%) number of N's = 20,112 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 15,350,893 number of insertions = 244,053 mapped reads with insertion percentage = 0.98% number of deletions = 571,912 mapped reads with deletion percentage = 2.32% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.6935X std coverageData = 11.675X There is a 24.44% of reference with a coverageData >= 1X There is a 13.43% of reference with a coverageData >= 2X There is a 8.08% of reference with a coverageData >= 3X There is a 5.24% of reference with a coverageData >= 4X There is a 3.55% of reference with a coverageData >= 5X There is a 2.5% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.33% of reference with a coverageData >= 8X There is a 1% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158894245 0.6374878600603366 3.9515808533444345 chr2 243199373 176859171 0.7272188608808625 5.879010449899697 chr3 198022430 139103135 0.7024615090320829 2.3353417377550403 chr4 191154276 122421117 0.6404309626848211 4.045957673849956 chr5 180915260 122781199 0.6786669018412267 1.8630982997395737 chr6 171115067 108079772 0.6316204288427739 2.6522933733190746 chr7 159138663 152805324 0.9602023865187306 6.777932688401938 chr8 146364022 82217014 0.5617296715172257 1.9084496125108794 chr9 141213431 88700216 0.6281287507276839 5.047542794791848 chr10 135534747 139519757 1.02940212814947 45.69102976988746 chr11 135006516 99527415 0.737204528705859 6.17190204967166 chr12 133851895 126875586 0.9478803867513419 2.3556548405625644 chr13 115169878 51163891 0.44424715809805754 1.3980203467187957 chr14 107349540 49255849 0.45883614405799966 1.745634960375285 chr15 102531392 76085695 0.7420721938506404 1.9738869580694847 chr16 90354753 93355419 1.0332098301458474 32.07028573139301 chr17 81195210 46534874 0.5731233899142573 3.1905963493735863 chr18 78077248 38991043 0.49939059071344316 5.404114008227156 chr19 59128983 17194455 0.29079571688219297 2.729032260736447 chr20 63025520 56227758 0.8921427066369305 2.356818845381965 chr21 48129895 17351906 0.36052241543431585 2.1692410934126563 chr22 51304566 13575276 0.26460171205814315 1.600583601605483 chrMT 16571 1032174 62.28797296481805 36.8696733003275 chrX 155270560 145271605 0.9356030209461471 3.8869124782158626 chrY 59373566 22901772 0.38572337056527817 6.695786913011546