BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975194.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 40,279,236 number of mapped reads = 39,894,818 (99.05%) number of supplementary alignments = 96,326 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,914,753 number of mapped paired reads (second in pair) = 19,980,065 number of mapped paired reads (both in pair) = 39,595,170 number of mapped paired reads (singletons) = 299,648 number of mapped bases = 3,715,515,239 bp number of sequenced bases = 3,714,122,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,313,896 duplication rate = 41.79% >>>>>>> Insert size mean insert size = 184,746.2427 std insert size = 4,262,327.9196 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.6378 >>>>>>> ACTG content number of A's = 1,007,112,093 bp (27.12%) number of C's = 809,931,215 bp (21.81%) number of T's = 1,014,568,192 bp (27.32%) number of G's = 882,263,693 bp (23.75%) number of N's = 247,508 bp (0.01%) GC percentage = 45.56% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 22,255,389 number of insertions = 413,201 mapped reads with insertion percentage = 1.02% number of deletions = 942,276 mapped reads with deletion percentage = 2.32% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 1.2002X std coverageData = 17.2892X There is a 9.48% of reference with a coverageData >= 1X There is a 4.42% of reference with a coverageData >= 2X There is a 2.76% of reference with a coverageData >= 3X There is a 2.19% of reference with a coverageData >= 4X There is a 1.91% of reference with a coverageData >= 5X There is a 1.74% of reference with a coverageData >= 6X There is a 1.62% of reference with a coverageData >= 7X There is a 1.53% of reference with a coverageData >= 8X There is a 1.46% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.33% of reference with a coverageData >= 11X There is a 1.28% of reference with a coverageData >= 12X There is a 1.24% of reference with a coverageData >= 13X There is a 1.19% of reference with a coverageData >= 14X There is a 1.16% of reference with a coverageData >= 15X There is a 1.12% of reference with a coverageData >= 16X There is a 1.08% of reference with a coverageData >= 17X There is a 1.05% of reference with a coverageData >= 18X There is a 1.02% of reference with a coverageData >= 19X There is a 1% of reference with a coverageData >= 20X There is a 0.97% of reference with a coverageData >= 21X There is a 0.94% of reference with a coverageData >= 22X There is a 0.92% of reference with a coverageData >= 23X There is a 0.9% of reference with a coverageData >= 24X There is a 0.88% of reference with a coverageData >= 25X There is a 0.86% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.78% of reference with a coverageData >= 30X There is a 0.77% of reference with a coverageData >= 31X There is a 0.75% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.71% of reference with a coverageData >= 35X There is a 0.69% of reference with a coverageData >= 36X There is a 0.68% of reference with a coverageData >= 37X There is a 0.67% of reference with a coverageData >= 38X There is a 0.65% of reference with a coverageData >= 39X There is a 0.64% of reference with a coverageData >= 40X There is a 0.63% of reference with a coverageData >= 41X There is a 0.62% of reference with a coverageData >= 42X There is a 0.61% of reference with a coverageData >= 43X There is a 0.6% of reference with a coverageData >= 44X There is a 0.59% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 517678322 2.0769389457208214 26.23230597046204 chr2 243199373 231107278 0.9502790864514277 13.219803555746855 chr3 198022430 266429396 1.3454505936524463 17.86760917259804 chr4 191154276 147997543 0.7742308783089947 12.769410678992106 chr5 180915260 263609445 1.4570879482471517 19.409563666160782 chr6 171115067 213742365 1.249114813483958 18.414701793998113 chr7 159138663 150111146 0.9432726351358124 14.71201394145882 chr8 146364022 160372875 1.095712408067059 16.37236675162775 chr9 141213431 123180686 0.8723014880928712 12.602672498696144 chr10 135534747 137346999 1.0133711246755048 14.4558522178147 chr11 135006516 175582292 1.30054679731162 15.912352239088957 chr12 133851895 175866593 1.3138894522188125 17.114093790282826 chr13 115169878 48735442 0.423161358215557 9.648353459915324 chr14 107349540 122117092 1.1375651167205747 16.696891079316973 chr15 102531392 105162515 1.0256616334634372 13.625614975454933 chr16 90354753 101945039 1.1282753326767436 14.90022072524968 chr17 81195210 118038187 1.4537580110944968 15.694480785063364 chr18 78077248 56084693 0.7183231278848353 11.513128113793561 chr19 59128983 150487724 2.5450754666286075 28.687183484058426 chr20 63025520 71037460 1.1271221562313172 16.449198173372388 chr21 48129895 29646668 0.6159720065875897 9.806956009305246 chr22 51304566 46986534 0.9158353274053619 12.628842429051591 chrMT 16571 89492 5.40051897893911 10.48461195038015 chrX 155270560 300386300 1.934599192532055 25.813847790911147 chrY 59373566 1773153 0.029864350744908938 1.7505714013308544