BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238053.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 = 2,119,940 number of mapped reads = 1,902,340 (89.74%) number of supplementary alignments = 21,300 (1%) number of secondary alignments = 0 number of mapped bases = 128,625,828 bp number of sequenced bases = 128,578,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,879 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5148 >>>>>>> ACTG content number of A's = 35,179,027 bp (27.36%) number of C's = 24,725,897 bp (19.23%) number of T's = 39,825,588 bp (30.97%) number of G's = 28,830,105 bp (22.42%) number of N's = 17,540 bp (0.01%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 943,079 number of insertions = 9,023 mapped reads with insertion percentage = 0.47% number of deletions = 26,973 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.4473X There is a 3.24% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 9399720 0.0377119220898551 0.9294800440056893 chr2 243199373 9154853 0.03764340708230362 0.4781420373996405 chr3 198022430 9641064 0.0486867270541019 0.27196766820456986 chr4 191154276 7456209 0.03900623703547181 0.25553848855912564 chr5 180915260 6851347 0.037870475934423664 0.24135040873405714 chr6 171115067 7139298 0.041722205561243765 0.30286332900800106 chr7 159138663 6893726 0.04331898905044841 0.5052305700671771 chr8 146364022 6748679 0.046108865469684894 0.41713256480509536 chr9 141213431 6328186 0.044812918680518427 0.4490417702363357 chr10 135534747 5821059 0.04294883141664034 0.43125705447729523 chr11 135006516 5760118 0.04266548142017086 0.3753008393128098 chr12 133851895 7338213 0.05482337773402461 0.30212771905569447 chr13 115169878 3318103 0.028810510678842605 0.20782711040412002 chr14 107349540 4252590 0.03961442219500894 0.28712544531035683 chr15 102531392 4567407 0.04454642535234477 0.25992272522630083 chr16 90354753 3163212 0.0350088057902167 0.2898129741872901 chr17 81195210 3766040 0.046382539068499234 0.29893593086200304 chr18 78077248 3541119 0.045354044753216714 0.8724198788723206 chr19 59128983 3099167 0.05241366995945119 0.6114005703806457 chr20 63025520 1858175 0.029482898356094484 0.2223694522484071 chr21 48129895 2008180 0.04172417164010019 0.2937506051889001 chr22 51304566 1573626 0.03067224075143721 0.2134439195889288 chrMT 16571 40301 2.432019793615352 2.2189003096181885 chrX 155270560 8511194 0.054815246367373185 0.31944098111800934 chrY 59373566 394242 0.006640025630261117 0.1355061052023126