BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714225.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 = 5,554 number of mapped reads = 1,540 (27.73%) number of supplementary alignments = 82 (1.48%) number of secondary alignments = 0 number of mapped bases = 175,721 bp number of sequenced bases = 172,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 751 duplication rate = 34.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 20.9378 >>>>>>> ACTG content number of A's = 38,778 bp (22.5%) number of C's = 31,212 bp (18.11%) number of T's = 35,853 bp (20.8%) number of G's = 66,527 bp (38.6%) number of N's = 2 bp (0%) GC percentage = 56.7% >>>>>>> Mismatches and indels general error rate = 0.0377 number of mismatches = 6,023 number of insertions = 101 mapped reads with insertion percentage = 4.81% number of deletions = 402 mapped reads with deletion percentage = 25.19% homopolymer indels = 33.2% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.0459X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 4254 1.706715908242411E-5 0.005582933435253164 chr2 243199373 42053 1.7291574185102854E-4 0.15191168378704303 chr3 198022430 3427 1.730612032182415E-5 0.0060503446399472385 chr4 191154276 3252 1.70124365933619E-5 0.006539989158877159 chr5 180915260 1819 1.0054431008196876E-5 0.00585028783886182 chr6 171115067 4706 2.7501961589390606E-5 0.009584741194985773 chr7 159138663 5914 3.716255929585132E-5 0.015145618906738644 chr8 146364022 8836 6.037002727350578E-5 0.035215969763118714 chr9 141213431 1464 1.036728581433589E-5 0.004442520426772634 chr10 135534747 2675 1.973663624428354E-5 0.007319330011546774 chr11 135006516 2200 1.629550976635824E-5 0.006269095899885751 chr12 133851895 3828 2.8598773293422554E-5 0.008129401360532465 chr13 115169878 1225 1.0636461731773302E-5 0.004275188345853892 chr14 107349540 3075 2.864474314468418E-5 0.01161723917792908 chr15 102531392 1802 1.757510519314904E-5 0.006577575574757907 chr16 90354753 978 1.0824001699169051E-5 0.004117677987135315 chr17 81195210 2105 2.592517465008096E-5 0.0076525744557206276 chr18 78077248 692 8.86301730306888E-6 0.003857799649040282 chr19 59128983 1867 3.157503994276377E-5 0.008474967866512565 chr20 63025520 2468 3.915874077675202E-5 0.017581562688849712 chr21 48129895 528 1.097031273390478E-5 0.004217236492056455 chr22 51304566 346 6.744039117298059E-6 0.003414064916987992 chrMT 16571 0 0.0 0.0 chrX 155270560 75473 4.8607411475813574E-4 0.0607021738059595 chrY 59373566 734 1.2362403834730089E-5 0.004087495966404837