BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094137.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 442,756 number of mapped reads = 430,876 (97.32%) number of supplementary alignments = 5,620 (1.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 216,143 number of mapped paired reads (second in pair) = 214,733 number of mapped paired reads (both in pair) = 428,886 number of mapped paired reads (singletons) = 1,990 number of mapped bases = 63,398,489 bp number of sequenced bases = 63,339,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 430,247 duplication rate = 40.61% >>>>>>> Insert size mean insert size = 105,414.052 std insert size = 3,857,221.6222 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 25.0743 >>>>>>> ACTG content number of A's = 17,853,602 bp (28.19%) number of C's = 13,464,191 bp (21.26%) number of T's = 18,150,767 bp (28.66%) number of G's = 13,870,193 bp (21.9%) number of N's = 766 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 949,587 number of insertions = 22,043 mapped reads with insertion percentage = 5.06% number of deletions = 41,217 mapped reads with deletion percentage = 9.33% homopolymer indels = 61.28% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 32.5601X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 861759 0.003457399610651321 4.170676750545505 chr2 243199373 4580461 0.018834180958188573 15.22508410532334 chr3 198022430 256723 0.0012964339443769072 0.8306742014055292 chr4 191154276 178452 9.335496109958848E-4 0.5189767303551354 chr5 180915260 86936 4.8053436730544454E-4 0.29319221069606394 chr6 171115067 155488 9.086750963899631E-4 0.43776562629046334 chr7 159138663 51470 3.2342863154505703E-4 0.1298710020774939 chr8 146364022 18746 1.2807792341208005E-4 0.03279534845027448 chr9 141213431 54712 3.87441899913897E-4 0.1548200779883146 chr10 135534747 66037 4.8723298978084196E-4 0.21410812471167298 chr11 135006516 30234 2.2394474648912503E-4 0.06876279624084396 chr12 133851895 203204 0.0015181256866030922 0.7996264455131709 chr13 115169878 265126 0.0023020429004882684 1.306828224186652 chr14 107349540 29334 2.732568765548506E-4 0.09561256414543758 chr15 102531392 544483 0.005310402886171681 3.75255400678448 chr16 90354753 97858 0.0010830420841281033 0.5019802387850827 chr17 81195210 307291 0.0037845951750109397 1.9246500701692562 chr18 78077248 28757 3.683147233877915E-4 0.20895300645060924 chr19 59128983 14149 2.3929043393152897E-4 0.08833480005893891 chr20 63025520 10307 1.635369291677403E-4 0.029670376439025165 chr21 48129895 4015 8.34200864140676E-5 0.01646804986144509 chr22 51304566 6464 1.2599268454975332E-4 0.041413701158049085 chrMT 16571 54126178 3266.319353086718 13544.14361976702 chrX 155270560 1409846 0.009079931185924749 4.049785873989373 chrY 59373566 10459 1.7615583338888554E-4 0.05295768993195868