BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238315.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,718,845 number of mapped reads = 3,376,152 (90.78%) number of supplementary alignments = 24,482 (0.66%) number of secondary alignments = 0 number of mapped bases = 216,606,171 bp number of sequenced bases = 216,504,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,655 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6738 >>>>>>> ACTG content number of A's = 58,860,515 bp (27.19%) number of C's = 41,437,055 bp (19.14%) number of T's = 65,763,959 bp (30.38%) number of G's = 50,387,298 bp (23.27%) number of N's = 55,427 bp (0.03%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,819,310 number of insertions = 16,822 mapped reads with insertion percentage = 0.49% number of deletions = 62,431 mapped reads with deletion percentage = 1.83% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.07X std coverageData = 0.4801X There is a 5.72% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15738134 0.06314180456946585 0.7041687568050196 chr2 243199373 27050258 0.11122667655890708 0.7536301683970734 chr3 198022430 12364234 0.06243855304674324 0.2924547231583632 chr4 191154276 8734212 0.04569195198123635 0.2777232089860786 chr5 180915260 11800846 0.06522858270772737 0.3018041850068668 chr6 171115067 12355908 0.07220818257926989 0.42371878951190495 chr7 159138663 7069560 0.044423899677980834 0.42729037078468035 chr8 146364022 14238469 0.09728120890255393 0.671259753326088 chr9 141213431 6889490 0.04878778138320285 0.43752399039651274 chr10 135534747 11874309 0.08761081023746627 0.4853284247333946 chr11 135006516 9074279 0.06721363730325432 0.44005249551780773 chr12 133851895 9221480 0.06889315986150214 0.31419530263593193 chr13 115169878 7933217 0.06888274206559461 0.31013059345371 chr14 107349540 4515506 0.042063580337652125 0.2920968912184329 chr15 102531392 6212259 0.06058884873034787 0.3031941326059063 chr16 90354753 6989111 0.07735189094036923 0.36342600140257497 chr17 81195210 6714653 0.0826976492825131 0.38223614827268243 chr18 78077248 6117776 0.07835542564205132 0.8307970197417248 chr19 59128983 4387146 0.07419620256279395 0.5878775231011142 chr20 63025520 4496288 0.07134075212707487 0.33178744300569263 chr21 48129895 2556776 0.05312240967905706 0.307460537644291 chr22 51304566 2424719 0.047261271053340555 0.2557031907773917 chrMT 16571 13007 0.7849254722104883 1.0628264613692973 chrX 155270560 17225997 0.11094181021824098 0.46403563264266107 chrY 59373566 608537 0.0102492917471051 0.1890284613061103