BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714140.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 690,544 number of mapped reads = 565,057 (81.83%) number of supplementary alignments = 20,367 (2.95%) number of secondary alignments = 0 number of mapped bases = 72,171,937 bp number of sequenced bases = 70,779,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 471,315 duplication rate = 43.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5755 >>>>>>> ACTG content number of A's = 19,515,641 bp (27.57%) number of C's = 15,421,907 bp (21.79%) number of T's = 18,466,281 bp (26.09%) number of G's = 17,375,463 bp (24.55%) number of N's = 526 bp (0%) GC percentage = 46.34% >>>>>>> Mismatches and indels general error rate = 0.0422 number of mismatches = 2,739,979 number of insertions = 79,838 mapped reads with insertion percentage = 13.72% number of deletions = 239,082 mapped reads with deletion percentage = 40.36% homopolymer indels = 28.43% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 2.663X There is a 0.07% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 6336344 0.02542157758555795 2.58512117974744 chr2 243199373 7131492 0.029323644678968808 5.265142896165357 chr3 198022430 3702902 0.01869940693082092 1.8026636619715222 chr4 191154276 3371232 0.01763618408410597 1.8693989329450764 chr5 180915260 4095993 0.02264039528782702 2.1500441642765153 chr6 171115067 2830293 0.016540290984428625 1.472248303291417 chr7 159138663 3015354 0.018947966152009207 1.9677017964978043 chr8 146364022 3535064 0.024152547543412 2.8517694309047408 chr9 141213431 2556953 0.01810700994865 1.975941955225058 chr10 135534747 4069412 0.030024861447522384 2.542020030707515 chr11 135006516 3255075 0.02411050293305843 2.3419096902987335 chr12 133851895 2983132 0.022286811852757108 2.127249729416475 chr13 115169878 2019953 0.017538900232229124 2.022222701251398 chr14 107349540 2463493 0.02294833308088698 2.3156946089377337 chr15 102531392 2299897 0.022431149671702497 2.1501611019709825 chr16 90354753 2430845 0.02690334397793108 2.8023769133167895 chr17 81195210 2651723 0.03265861372856847 3.1151921489667713 chr18 78077248 1802579 0.023087122640388143 2.14904953131548 chr19 59128983 1601499 0.027084839257255616 2.6403510197883704 chr20 63025520 1949198 0.03092712285436122 2.5042860861819447 chr21 48129895 659123 0.013694669394146819 1.549718213621846 chr22 51304566 803068 0.015652953774133865 1.5724772498650457 chrMT 16571 462675 27.92076519220325 257.82145200873657 chrX 155270560 5850888 0.03768188895563976 2.367061865427558 chrY 59373566 293750 0.004947487910697498 0.7601394997746754