BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472644.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 = 9,698,970 number of mapped reads = 9,615,790 (99.14%) number of supplementary alignments = 49,136 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,814,293 number of mapped paired reads (second in pair) = 4,801,497 number of mapped paired reads (both in pair) = 9,564,072 number of mapped paired reads (singletons) = 51,718 number of mapped bases = 942,431,829 bp number of sequenced bases = 942,304,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,376,742 duplication rate = 42.93% >>>>>>> Insert size mean insert size = 21,500.7591 std insert size = 1,435,704.672 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 54.6191 >>>>>>> ACTG content number of A's = 259,259,561 bp (27.51%) number of C's = 213,364,461 bp (22.64%) number of T's = 260,099,774 bp (27.6%) number of G's = 209,458,475 bp (22.23%) number of N's = 122,181 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 7,056,873 number of insertions = 60,061 mapped reads with insertion percentage = 0.62% number of deletions = 58,084 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.3044X std coverageData = 18.2946X There is a 2.38% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.18% 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 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 116871630 0.468892031366293 23.449861335744963 chr2 243199373 69970597 0.28770878862422067 14.63058775013207 chr3 198022430 81565705 0.4119013437013171 17.999062875536488 chr4 191154276 37127397 0.19422739463071179 13.476061815776534 chr5 180915260 49812095 0.27533384967083485 16.677565357545898 chr6 171115067 44351641 0.2591919097340505 10.09119121199055 chr7 159138663 79444057 0.49921279657854106 30.22820263947044 chr8 146364022 47576288 0.325054527402916 16.736406063070902 chr9 141213431 36140609 0.2559289774639071 17.784157377288004 chr10 135534747 19501370 0.14388465269352663 6.799236798443234 chr11 135006516 31725635 0.23499336135746218 10.190575084148058 chr12 133851895 31177570 0.2329258767684985 8.072183486322023 chr13 115169878 38882881 0.33761328634905735 31.452223724838895 chr14 107349540 18231810 0.16983593967892177 6.796972019397421 chr15 102531392 21611379 0.21077816830966267 13.785982351689794 chr16 90354753 48265308 0.5341756398802839 20.80247088526967 chr17 81195210 82354899 1.0142827267766166 49.702111571093425 chr18 78077248 10263648 0.13145504308758424 8.175578381615756 chr19 59128983 13830319 0.2339008435169602 7.20728142766166 chr20 63025520 11567089 0.18353024298728515 8.257923680939085 chr21 48129895 6587514 0.13686948621018183 7.540683783032799 chr22 51304566 18821635 0.3668608170274747 19.285572466732482 chrMT 16571 3068 0.1851427192082554 0.5007978751006567 chrX 155270560 25151282 0.1619835852978182 6.987584634395136 chrY 59373566 1596403 0.02688743674247223 1.6778457845879347