BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240013.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 = 1,214,487 number of mapped reads = 976,101 (80.37%) number of supplementary alignments = 4,126 (0.34%) number of secondary alignments = 0 number of mapped bases = 61,403,398 bp number of sequenced bases = 61,367,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,932 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7171 >>>>>>> ACTG content number of A's = 16,778,050 bp (27.34%) number of C's = 10,707,763 bp (17.45%) number of T's = 19,147,084 bp (31.2%) number of G's = 14,695,635 bp (23.95%) number of N's = 38,776 bp (0.06%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 638,891 number of insertions = 4,473 mapped reads with insertion percentage = 0.46% number of deletions = 20,308 mapped reads with deletion percentage = 2.06% homopolymer indels = 49.61% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.2189X There is a 1.76% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4978166 0.0199725319841831 0.3111915044706645 chr2 243199373 7444474 0.030610580562639857 0.2638055683160669 chr3 198022430 4086467 0.02063638447422345 0.1587325401568109 chr4 191154276 3631733 0.018998962910984005 0.16156786950525093 chr5 180915260 3216190 0.0177773284575331 0.1481885972928814 chr6 171115067 3407486 0.01991341884581093 0.18281365582944967 chr7 159138663 4237407 0.026627137115007683 0.4565104787431876 chr8 146364022 3329304 0.02274673758281936 0.25059902526888816 chr9 141213431 2018332 0.014292776442773351 0.18952234087069422 chr10 135534747 3020777 0.02228784180340116 0.18731972660392218 chr11 135006516 2234475 0.01655086781144697 0.16781368319436882 chr12 133851895 2826765 0.021118602766139395 0.16081004515446268 chr13 115169878 877135 0.007616010498856307 0.09652580479463095 chr14 107349540 2035284 0.018959410538694436 0.15852375748049874 chr15 102531392 1814012 0.01769225955695598 0.17434434970958135 chr16 90354753 1929745 0.021357426542906933 0.16414188447590228 chr17 81195210 1775498 0.021867028855519926 0.17599254011899657 chr18 78077248 1229979 0.015753360056952825 0.24889919577340572 chr19 59128983 1404530 0.02375366408720407 0.2367259292375417 chr20 63025520 1173611 0.018621202966671278 0.153383027402988 chr21 48129895 1080309 0.02244569617282564 0.17145300491702387 chr22 51304566 492450 0.009598560876628408 0.10562906101113287 chrMT 16571 14340 0.8653672077726148 1.268863631881615 chrX 155270560 3017326 0.01943269863907234 0.16711179019858652 chrY 59373566 127603 0.0021491550633829203 0.05416736816819398