BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714082.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 = 457,842 number of mapped reads = 260,587 (56.92%) number of supplementary alignments = 9,693 (2.12%) number of secondary alignments = 0 number of mapped bases = 33,814,433 bp number of sequenced bases = 33,067,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 226,561 duplication rate = 41.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9043 >>>>>>> ACTG content number of A's = 8,925,446 bp (26.99%) number of C's = 6,753,571 bp (20.42%) number of T's = 8,483,789 bp (25.66%) number of G's = 8,904,527 bp (26.93%) number of N's = 289 bp (0%) GC percentage = 47.35% >>>>>>> Mismatches and indels general error rate = 0.0452 number of mismatches = 1,382,092 number of insertions = 37,429 mapped reads with insertion percentage = 13.59% number of deletions = 124,318 mapped reads with deletion percentage = 44.13% homopolymer indels = 31.32% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 3.1089X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 2353909 0.00944394437436527 1.7644056586176755 chr2 243199373 4563221 0.018763292617534833 8.519554551042097 chr3 198022430 1619288 0.008177295875017795 2.062866254276925 chr4 191154276 1198642 0.006270547670092402 1.0630755777054595 chr5 180915260 1273998 0.0070419598656299084 1.0692155612569285 chr6 171115067 1074703 0.006280586618360147 0.8208814983192634 chr7 159138663 1584214 0.009954928426161278 1.6074502336319045 chr8 146364022 2988067 0.020415310806367427 5.720339108362914 chr9 141213431 1309402 0.009272503264933772 1.794103823034103 chr10 135534747 1746316 0.012884636882083087 1.6880381420261896 chr11 135006516 1472607 0.010907673522957958 2.2593492151337924 chr12 133851895 1316206 0.009833301202048728 1.4120222508849019 chr13 115169878 1018284 0.008841582692307793 1.493569477585929 chr14 107349540 861428 0.008024515056142765 1.4537866647753346 chr15 102531392 892518 0.008704826712973915 1.2280095200662835 chr16 90354753 772814 0.008553108434705145 1.13802613073015 chr17 81195210 997124 0.012280576649780203 2.4779422825149893 chr18 78077248 868935 0.011129170433875948 1.7841224972745977 chr19 59128983 688139 0.011637930589809062 1.709993891018672 chr20 63025520 701166 0.011125112494113496 1.8091582156597628 chr21 48129895 247217 0.0051364541726093525 0.8355116392810018 chr22 51304566 350525 0.006832237894771393 0.850380583552728 chrMT 16571 353501 21.332508599360327 156.2885028820805 chrX 155270560 3458418 0.022273494730746125 2.1556780767960135 chrY 59373566 103791 0.0017481011667717582 0.680561998288551