BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094125.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 19,726 number of mapped reads = 1,112 (5.64%) number of supplementary alignments = 53 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 491 number of mapped paired reads (second in pair) = 621 number of mapped paired reads (both in pair) = 888 number of mapped paired reads (singletons) = 224 number of mapped bases = 109,960 bp number of sequenced bases = 107,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 503 duplication rate = 25.98% >>>>>>> Insert size mean insert size = 1,025,216.4976 std insert size = 8,254,894.3909 median insert size = 131 >>>>>>> Mapping quality mean mapping quality = 15.4016 >>>>>>> ACTG content number of A's = 27,121 bp (25.12%) number of C's = 19,213 bp (17.79%) number of T's = 23,725 bp (21.97%) number of G's = 37,914 bp (35.11%) number of N's = 0 bp (0%) GC percentage = 52.91% >>>>>>> Mismatches and indels general error rate = 0.0396 number of mismatches = 3,880 number of insertions = 93 mapped reads with insertion percentage = 6.56% number of deletions = 273 mapped reads with deletion percentage = 23.56% homopolymer indels = 36.61% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0242X 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 1467 5.885642306985466E-6 0.003612073449908819 chr2 243199373 21620 8.889825550660446E-5 0.07620581472429519 chr3 198022430 2499 1.261978251655633E-5 0.006081989916772921 chr4 191154276 2051 1.0729553337326339E-5 0.004597813066013258 chr5 180915260 1135 6.273655411931531E-6 0.0030006967163382493 chr6 171115067 1063 6.212194043672378E-6 0.0036494501320294896 chr7 159138663 2054 1.2906982886993339E-5 0.006009932333372134 chr8 146364022 1604 1.095897733665723E-5 0.004076271541715746 chr9 141213431 2005 1.4198366159660833E-5 0.005321526444799944 chr10 135534747 1456 1.0742632662309097E-5 0.004061711343945118 chr11 135006516 4277 3.167995239577918E-5 0.010231465396206823 chr12 133851895 2815 2.1030707111019983E-5 0.009537597828993036 chr13 115169878 1172 1.0176271958888417E-5 0.004670241894621113 chr14 107349540 939 8.747126443205998E-6 0.0054195263305033305 chr15 102531392 736 7.178289357468199E-6 0.003477615444864942 chr16 90354753 1387 1.535060363675611E-5 0.005617222608329688 chr17 81195210 1838 2.2636803328669266E-5 0.008457589939115944 chr18 78077248 554 7.09553697384416E-6 0.0033875901276501173 chr19 59128983 283 4.7861469222293235E-6 0.0029050223547269784 chr20 63025520 158 2.5069210059671066E-6 0.002239159602904912 chr21 48129895 252 5.235831077545463E-6 0.0029328646526241035 chr22 51304566 140 2.7288019549760934E-6 0.0016519063256177646 chrMT 16571 2249 0.13571902721622112 0.9057899806103813 chrX 155270560 54020 3.479088373224132E-4 0.043800793934125136 chrY 59373566 2186 3.6817731311607595E-5 0.009752355238849656