BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818807.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,167,502 number of mapped reads = 3,089,888 (97.55%) number of supplementary alignments = 22,290 (0.7%) number of secondary alignments = 0 number of mapped bases = 210,058,005 bp number of sequenced bases = 209,970,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,685,257 duplication rate = 44.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.642 >>>>>>> ACTG content number of A's = 59,000,886 bp (28.1%) number of C's = 44,722,222 bp (21.3%) number of T's = 60,130,904 bp (28.64%) number of G's = 46,104,153 bp (21.96%) number of N's = 12,423 bp (0.01%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,044,528 number of insertions = 20,129 mapped reads with insertion percentage = 0.64% number of deletions = 52,692 mapped reads with deletion percentage = 1.69% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0679X std coverageData = 0.8582X There is a 2.55% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 17428718 0.06992447172278059 1.279080672650586 chr2 243199373 18416653 0.07572656447597009 1.459978310430695 chr3 198022430 13961291 0.07050358386168679 0.5692291424805498 chr4 191154276 13564174 0.0709593020037909 0.7037690694096024 chr5 180915260 12980681 0.07175006132705444 0.6059285152528603 chr6 171115067 12295881 0.07185738354647636 0.6564997027241374 chr7 159138663 11703381 0.07354203421955355 0.7155318535997404 chr8 146364022 10852325 0.07414612451685702 0.6777088864006866 chr9 141213431 8985789 0.06363267952890402 0.6510491176522225 chr10 135534747 10049451 0.07414667620252392 0.9419074296895588 chr11 135006516 9945823 0.07366920719589565 0.6712336562938108 chr12 133851895 9602715 0.07174134516362282 0.6197319617858561 chr13 115169878 6446597 0.055974679420950677 0.505413282739717 chr14 107349540 6400063 0.05961891406334857 0.6223554217744146 chr15 102531392 6188396 0.06035611025353094 0.5394174214038313 chr16 90354753 6467972 0.07158419214537613 1.0288030948084175 chr17 81195210 5810183 0.07155819906125004 0.6353550050466304 chr18 78077248 5623236 0.0720214421491905 0.8598241427456448 chr19 59128983 4466524 0.0755386575818495 1.094719151684667 chr20 63025520 4615264 0.0732284953777454 0.6423475651462204 chr21 48129895 2896619 0.06018336420638358 0.5648621012018199 chr22 51304566 2572064 0.05013323765374021 0.556168634462883 chrMT 16571 131160 7.915032285317723 7.957121363172186 chrX 155270560 6572578 0.0423298402478873 0.5290690564926186 chrY 59373566 2080467 0.0350402904888684 1.605961342152012