BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124820.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 = 24,966,532 number of mapped reads = 23,549,231 (94.32%) number of supplementary alignments = 32,824 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,877,812 number of mapped paired reads (second in pair) = 11,671,419 number of mapped paired reads (both in pair) = 23,106,100 number of mapped paired reads (singletons) = 443,131 number of mapped bases = 1,528,315,794 bp number of sequenced bases = 1,527,565,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,243,318 duplication rate = 8.93% >>>>>>> Insert size mean insert size = 37,681.9012 std insert size = 1,854,691.6048 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 52.0347 >>>>>>> ACTG content number of A's = 427,644,876 bp (28%) number of C's = 281,307,735 bp (18.42%) number of T's = 454,269,719 bp (29.74%) number of G's = 364,297,298 bp (23.85%) number of N's = 45,928 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 12,397,733 number of insertions = 183,758 mapped reads with insertion percentage = 0.77% number of deletions = 497,438 mapped reads with deletion percentage = 2.09% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.4937X std coverageData = 2.9832X There is a 23.03% of reference with a coverageData >= 1X There is a 10.89% of reference with a coverageData >= 2X There is a 5.63% of reference with a coverageData >= 3X There is a 3.1% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 123136058 0.4940250800819469 3.045271770567222 chr2 243199373 130151165 0.5351624200116667 4.192379032913752 chr3 198022430 93506470 0.47220140667903127 1.1911055566557762 chr4 191154276 83653431 0.4376225986176736 2.656418639426851 chr5 180915260 85619446 0.47325718129029026 1.2085735890363127 chr6 171115067 79102830 0.46227857889334784 1.9893436570839973 chr7 159138663 75204610 0.4725728404542396 3.7344843261424994 chr8 146364022 72758245 0.49710471197628064 1.59692331373004 chr9 141213431 59619400 0.42219355183006635 2.8923954015210187 chr10 135534747 73324698 0.5410029503356804 5.566165348629091 chr11 135006516 91301345 0.6762736177859742 3.5503397423146583 chr12 133851895 92887615 0.6939581617428726 2.658542549740161 chr13 115169878 65756152 0.5709492198993212 1.3627678982085227 chr14 107349540 43414620 0.4044229719102662 1.3262047210832693 chr15 102531392 40623815 0.39620855825306656 1.1333033635720549 chr16 90354753 47703431 0.5279570738243289 4.895038312406663 chr17 81195210 41739128 0.5140589943667859 3.21984838989224 chr18 78077248 38570837 0.4940086643422678 4.405562035092333 chr19 59128983 24428277 0.413135416179913 2.429109957493891 chr20 63025520 41295329 0.6552159982178648 1.6773404939656222 chr21 48129895 16884505 0.3508111746348086 1.8634279557795497 chr22 51304566 18879552 0.36798970290480576 1.1533215919407784 chrMT 16571 237859 14.353931567195703 8.568623775722662 chrX 155270560 84041342 0.541257415443082 2.117244984390074 chrY 59373566 4475634 0.07538091951559722 4.539250515187216