BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714098.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 = 535,102 number of mapped reads = 384,874 (71.93%) number of supplementary alignments = 11,815 (2.21%) number of secondary alignments = 0 number of mapped bases = 50,610,547 bp number of sequenced bases = 49,387,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,242 duplication rate = 43.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.5374 >>>>>>> ACTG content number of A's = 13,948,310 bp (28.24%) number of C's = 10,269,954 bp (20.79%) number of T's = 13,262,331 bp (26.85%) number of G's = 11,906,647 bp (24.11%) number of N's = 431 bp (0%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0472 number of mismatches = 2,175,782 number of insertions = 56,088 mapped reads with insertion percentage = 13.99% number of deletions = 196,187 mapped reads with deletion percentage = 47.29% homopolymer indels = 30.31% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 3.1084X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 3427218 0.013750088109108462 2.1555355094179856 chr2 243199373 5530701 0.022741427873664788 6.126451959285569 chr3 198022430 3364394 0.016989964217689883 3.4560588845942704 chr4 191154276 1743274 0.009119722752108355 1.1900549384047605 chr5 180915260 2912843 0.016100593172737335 2.9645081210575333 chr6 171115067 2005930 0.011722696517425902 1.6744800387406407 chr7 159138663 2546608 0.01600244687238575 2.820087677981241 chr8 146364022 2808097 0.019185705350458326 3.967345857373197 chr9 141213431 2017958 0.014290127969484716 2.8866525781381243 chr10 135534747 2960026 0.021839609882475377 2.9139897885601305 chr11 135006516 2650785 0.01963449675273451 3.4955146192909488 chr12 133851895 1912891 0.014291101369913366 1.8549800269402177 chr13 115169878 1669624 0.014497054516285933 2.246647397612324 chr14 107349540 1907041 0.01776478036142493 3.0575415421171814 chr15 102531392 1189010 0.011596545963210955 1.4007036409495441 chr16 90354753 939395 0.010396741386698273 1.1892418737313015 chr17 81195210 1035611 0.012754582443964367 2.253833160539876 chr18 78077248 1476122 0.018905917380694564 2.69013836485102 chr19 59128983 813615 0.013760003279609934 1.9713389634150162 chr20 63025520 1081266 0.017156002838215376 3.9477387070721406 chr21 48129895 319343 0.006635023824589686 0.8186688740300634 chr22 51304566 419754 0.008181610970064536 1.4743762856575282 chrMT 16571 183785 11.090760967956069 88.06288684020747 chrX 155270560 5401565 0.034788082170889315 3.961202499358187 chrY 59373566 293691 0.004946494202487349 1.2821547109477331