BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008690.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 = 1,431,359 number of mapped reads = 981,258 (68.55%) number of supplementary alignments = 4,071 (0.28%) number of secondary alignments = 0 number of mapped bases = 60,061,005 bp number of sequenced bases = 60,023,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,988 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2714 >>>>>>> ACTG content number of A's = 16,267,123 bp (27.1%) number of C's = 10,924,965 bp (18.2%) number of T's = 18,668,174 bp (31.1%) number of G's = 14,152,951 bp (23.58%) number of N's = 10,324 bp (0.02%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 592,928 number of insertions = 5,233 mapped reads with insertion percentage = 0.53% number of deletions = 23,392 mapped reads with deletion percentage = 2.35% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.1991X There is a 1.61% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 5234952 0.02100276412149842 0.25798881533323487 chr2 243199373 5359975 0.022039427708557456 0.24032566985310408 chr3 198022430 4171612 0.02106636101778975 0.17302288270711788 chr4 191154276 3476481 0.01818678123632453 0.16393706724833668 chr5 180915260 3379832 0.018681851381691074 0.16169286181429884 chr6 171115067 3385265 0.019783558861009007 0.1816013077926335 chr7 159138663 3285353 0.02064459345118414 0.2552376208000889 chr8 146364022 3396207 0.023203837620696156 0.22002366385875471 chr9 141213431 2423116 0.017159245992684646 0.18995044391502566 chr10 135534747 2697733 0.01990436445054197 0.20570181215789843 chr11 135006516 2682783 0.0198715075352363 0.20117054073426402 chr12 133851895 3092050 0.02310053212171557 0.18234204640073876 chr13 115169878 1904555 0.01653691948861837 0.15590272228854765 chr14 107349540 1672444 0.015579424001257947 0.15499005466107377 chr15 102531392 1834659 0.017893632030276153 0.1606785571283146 chr16 90354753 1645190 0.01820811795036394 0.19391569739993597 chr17 81195210 1418502 0.017470267026835698 0.167005629473904 chr18 78077248 1628684 0.02085990530813791 0.2863223378977414 chr19 59128983 1094613 0.01851229201760497 0.20854326527393718 chr20 63025520 1266860 0.020100746491262585 0.17022705259990875 chr21 48129895 838138 0.017414083284411904 0.16203845943889186 chr22 51304566 678217 0.01321942768212872 0.13445587226567038 chrMT 16571 37165 2.2427735200048278 2.1290807372123792 chrX 155270560 3268460 0.021050094750737037 0.18268778731546959 chrY 59373566 188159 0.003169070222260189 0.08121137675174796