BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714133.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 = 662,688 number of mapped reads = 549,257 (82.88%) number of supplementary alignments = 16,243 (2.45%) number of secondary alignments = 0 number of mapped bases = 71,089,125 bp number of sequenced bases = 69,501,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 488,386 duplication rate = 44.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6101 >>>>>>> ACTG content number of A's = 18,583,624 bp (26.74%) number of C's = 15,363,659 bp (22.11%) number of T's = 17,574,753 bp (25.29%) number of G's = 17,978,695 bp (25.87%) number of N's = 618 bp (0%) GC percentage = 47.97% >>>>>>> Mismatches and indels general error rate = 0.0444 number of mismatches = 2,869,394 number of insertions = 76,716 mapped reads with insertion percentage = 13.41% number of deletions = 249,257 mapped reads with deletion percentage = 43.15% homopolymer indels = 29.81% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 6.706X There is a 0.06% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 6434979 0.02581730378116089 7.051497468143574 chr2 243199373 8505808 0.03497462964265126 11.185387403461462 chr3 198022430 1976280 0.009980081549347718 1.4037410150876262 chr4 191154276 2712239 0.014188743546600024 3.2215165411891515 chr5 180915260 3566443 0.019713334298057553 3.5113118836341286 chr6 171115067 2793860 0.01632737577690923 3.144858892130039 chr7 159138663 2069931 0.013007090552218601 2.2208640019550794 chr8 146364022 2554482 0.017452936624001766 3.9906005057284886 chr9 141213431 2775835 0.019657018318604554 4.559176045120913 chr10 135534747 3305362 0.024387561663430854 3.729610916986537 chr11 135006516 3339266 0.02473410987066728 4.155429822037414 chr12 133851895 4142935 0.030951635014207307 6.805227249783358 chr13 115169878 2590431 0.022492261387999386 8.16778071719394 chr14 107349540 4846755 0.04514928522283374 22.60483927465074 chr15 102531392 2104406 0.020524504339119867 3.3387766360815454 chr16 90354753 1219991 0.013502233800583794 1.6778005522115191 chr17 81195210 2432031 0.02995288761492211 4.782146727671042 chr18 78077248 2130842 0.027291458838303317 5.482062554167521 chr19 59128983 1918257 0.032441907549805145 3.6027086383973894 chr20 63025520 1999447 0.031724403067201985 4.216080413703845 chr21 48129895 632211 0.013135515878436884 1.921121105447484 chr22 51304566 409920 0.00798993212417 1.0686229235049722 chrMT 16571 135372 8.16921127270533 68.88996852528224 chrX 155270560 5945123 0.038288797309676735 4.474641374497951 chrY 59373566 546919 0.009211489840445158 1.7494968498646821