BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617706.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 59,006,370 number of mapped reads = 58,237,631 (98.7%) number of supplementary alignments = 1,772,560 (3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,316,954 number of mapped paired reads (second in pair) = 28,920,677 number of mapped paired reads (both in pair) = 57,735,984 number of mapped paired reads (singletons) = 501,647 number of mapped bases = 7,749,635,408 bp number of sequenced bases = 7,743,704,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,167,045 duplication rate = 24.56% >>>>>>> Insert size mean insert size = 179,463.1166 std insert size = 4,003,530.3341 median insert size = 262 >>>>>>> Mapping quality mean mapping quality = 53.2986 >>>>>>> ACTG content number of A's = 2,281,071,819 bp (29.46%) number of C's = 1,427,141,116 bp (18.43%) number of T's = 2,372,079,703 bp (30.63%) number of G's = 1,663,103,918 bp (21.48%) number of N's = 308,049 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 84,793,132 number of insertions = 1,420,639 mapped reads with insertion percentage = 2.28% number of deletions = 2,955,224 mapped reads with deletion percentage = 4.86% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 2.5034X std coverageData = 31.4929X There is a 54.56% of reference with a coverageData >= 1X There is a 40.28% of reference with a coverageData >= 2X There is a 29.77% of reference with a coverageData >= 3X There is a 22.66% of reference with a coverageData >= 4X There is a 17.32% of reference with a coverageData >= 5X There is a 13.44% of reference with a coverageData >= 6X There is a 10.5% of reference with a coverageData >= 7X There is a 8.29% of reference with a coverageData >= 8X There is a 6.59% of reference with a coverageData >= 9X There is a 5.27% of reference with a coverageData >= 10X There is a 4.25% of reference with a coverageData >= 11X There is a 3.45% of reference with a coverageData >= 12X There is a 2.82% of reference with a coverageData >= 13X There is a 2.31% of reference with a coverageData >= 14X There is a 1.91% of reference with a coverageData >= 15X There is a 1.59% of reference with a coverageData >= 16X There is a 1.32% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.79% of reference with a coverageData >= 20X There is a 0.68% of reference with a coverageData >= 21X There is a 0.58% of reference with a coverageData >= 22X There is a 0.5% of reference with a coverageData >= 23X There is a 0.43% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 638132510 2.560204293332533 30.006382328464383 chr2 243199373 605504325 2.4897445973267374 34.50461454336734 chr3 198022430 438076857 2.2122587678577625 4.148299042973298 chr4 191154276 575459938 3.0104476344541724 25.219458305366494 chr5 180915260 477755603 2.6407700654991735 4.900952478978084 chr6 171115067 582100092 3.401805008789787 21.436253602210847 chr7 159138663 559988933 3.518874184584547 50.354264278566376 chr8 146364022 426801765 2.9160292206236313 9.071078580271823 chr9 141213431 360850468 2.5553551489022315 52.14252841987007 chr10 135534747 412416415 3.0428832762715823 81.7530682908426 chr11 135006516 297558778 2.20403271498392 28.992078647859913 chr12 133851895 276604274 2.0664950167496694 10.774589309380211 chr13 115169878 275735155 2.394160346336392 4.300650853415855 chr14 107349540 189206064 1.7625232860802198 4.641671715051633 chr15 102531392 229117350 2.2346068411906472 6.0951067191299595 chr16 90354753 206618393 2.286746254510817 41.429869961674385 chr17 81195210 158894550 1.9569448739648558 22.78002698733085 chr18 78077248 239017403 3.06129389960056 42.744246422379234 chr19 59128983 94066485 1.5908693203804978 15.647375099614884 chr20 63025520 160402194 2.545035630011462 8.425930365400413 chr21 48129895 104431368 2.169781754146773 11.916788364222677 chr22 51304566 53556480 1.043893052325986 3.899740042875088 chrMT 16571 1044290 63.019129805081164 35.81616177278057 chrX 155270560 266140352 1.7140425847630099 9.02365064290344 chrY 59373566 120155366 2.0237181980950916 46.02015651958195