BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 708,394 number of mapped reads = 600,593 (84.78%) number of supplementary alignments = 1,835 (0.26%) number of secondary alignments = 0 number of mapped bases = 35,191,268 bp number of sequenced bases = 35,179,827 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,576 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2525 >>>>>>> ACTG content number of A's = 9,139,274 bp (25.98%) number of C's = 6,213,065 bp (17.66%) number of T's = 11,122,143 bp (31.62%) number of G's = 8,702,106 bp (24.74%) number of N's = 3,239 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 168,873 number of insertions = 2,587 mapped reads with insertion percentage = 0.43% number of deletions = 7,110 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0114X std coverageData = 0.1369X There is a 1.05% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2784693 0.01117226103119719 0.21645117004672976 chr2 243199373 2995717 0.012317947053259878 0.15418935284518773 chr3 198022430 2363379 0.011934905555900915 0.1157250169891076 chr4 191154276 2292774 0.011994364175248688 0.12312501022884507 chr5 180915260 2141447 0.01183674058230356 0.11471713806173424 chr6 171115067 2046243 0.011958286525405738 0.12115277772230486 chr7 159138663 1911203 0.012009671087911553 0.15094729913573923 chr8 146364022 1786970 0.012209079632971551 0.14530637669868515 chr9 141213431 1491162 0.010559632957292852 0.12212518271018052 chr10 135534747 1709502 0.012613016498271104 0.14627679457820544 chr11 135006516 1583631 0.011730033830367121 0.12520671275859774 chr12 133851895 1572069 0.011744839324090256 0.11652739797319223 chr13 115169878 1088069 0.009447513697982732 0.10287675708974776 chr14 107349540 1091398 0.01016676922882017 0.1072662677169859 chr15 102531392 1021113 0.009959027962870142 0.10504215370430141 chr16 90354753 1019453 0.01128278221290694 0.11566476108585096 chr17 81195210 922649 0.011363342739060592 0.11640763196335013 chr18 78077248 939440 0.012032186380339635 0.1658571279534246 chr19 59128983 684155 0.011570552464939233 0.16871205879287765 chr20 63025520 748583 0.0118774585279106 0.11742397619481837 chr21 48129895 470130 0.009767941525739876 0.11252642119430828 chr22 51304566 410742 0.008005954089934217 0.09487424906276083 chrMT 16571 19957 1.20433287067769 1.3443309598553672 chrX 155270560 1978701 0.01274356838798031 0.12507668721786674 chrY 59373566 118088 0.0019888985613564125 0.07493171547547035