BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008762.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 = 1,724,958 number of mapped reads = 1,538,274 (89.18%) number of supplementary alignments = 14,705 (0.85%) number of secondary alignments = 0 number of mapped bases = 102,216,597 bp number of sequenced bases = 102,166,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,300 duplication rate = 5.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.809 >>>>>>> ACTG content number of A's = 27,469,415 bp (26.89%) number of C's = 19,936,192 bp (19.51%) number of T's = 31,316,553 bp (30.65%) number of G's = 23,313,796 bp (22.82%) number of N's = 130,404 bp (0.13%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 842,729 number of insertions = 7,979 mapped reads with insertion percentage = 0.51% number of deletions = 28,063 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3477X There is a 2.42% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.16% 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% 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 9510333 0.03815570433423313 0.5593761720579208 chr2 243199373 9712080 0.03993464243018423 0.47433666035763766 chr3 198022430 10082244 0.050914656486136446 0.30104066430814314 chr4 191154276 4784918 0.025031707896505544 0.21585967092310607 chr5 180915260 5859744 0.03238944022743023 0.23396052463748848 chr6 171115067 5866552 0.03428425154402096 0.26141448041067417 chr7 159138663 5897745 0.037060415670326446 0.36254889035088644 chr8 146364022 4255470 0.029074563146399463 0.5334376064044823 chr9 141213431 4287740 0.030363542402705307 0.2630125482858159 chr10 135534747 5351769 0.03948632449212452 0.43591425106343606 chr11 135006516 4142335 0.030682482021830708 0.2450244381186616 chr12 133851895 3942743 0.02945601181066581 0.22660918565114635 chr13 115169878 2518324 0.02186616886057655 0.19224717759265267 chr14 107349540 2677072 0.024937899128398687 0.2147162742004203 chr15 102531392 2581105 0.02517380238044559 0.204919574423609 chr16 90354753 2118666 0.023448307141075358 0.3058046858901921 chr17 81195210 3323079 0.04092703251829757 0.2829801421909088 chr18 78077248 1728650 0.022140252689234127 0.3387534726390702 chr19 59128983 2833403 0.04791902137061955 0.4166741028116143 chr20 63025520 2747798 0.04359818054654686 0.27763047009372427 chr21 48129895 1134104 0.023563400668129446 0.21369349511505897 chr22 51304566 1044885 0.020366315933751395 0.1842106151708983 chrMT 16571 402971 24.317844427011043 13.618891977553284 chrX 155270560 5130876 0.03304474460580293 0.2415005335651043 chrY 59373566 281991 0.00474943681166127 0.15309245546413494