BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514759.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 48,394,834 number of mapped reads = 44,894,947 (92.77%) number of supplementary alignments = 6,262,693 (12.94%) number of secondary alignments = 0 number of mapped bases = 4,306,495,933 bp number of sequenced bases = 4,304,163,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,993,466 duplication rate = 44.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5728 >>>>>>> ACTG content number of A's = 1,343,546,701 bp (31.22%) number of C's = 809,099,433 bp (18.8%) number of T's = 1,321,256,657 bp (30.7%) number of G's = 829,962,084 bp (19.28%) number of N's = 298,625 bp (0.01%) GC percentage = 38.08% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 20,761,113 number of insertions = 2,416,410 mapped reads with insertion percentage = 5.2% number of deletions = 870,391 mapped reads with deletion percentage = 1.86% homopolymer indels = 55.66% >>>>>>> Coverage mean coverageData = 1.3911X std coverageData = 45.2047X There is a 4.6% of reference with a coverageData >= 1X There is a 3.03% of reference with a coverageData >= 2X There is a 2.48% of reference with a coverageData >= 3X There is a 2.17% of reference with a coverageData >= 4X There is a 1.97% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.69% of reference with a coverageData >= 7X There is a 1.59% of reference with a coverageData >= 8X There is a 1.5% of reference with a coverageData >= 9X There is a 1.43% of reference with a coverageData >= 10X There is a 1.36% of reference with a coverageData >= 11X There is a 1.31% of reference with a coverageData >= 12X There is a 1.25% of reference with a coverageData >= 13X There is a 1.21% of reference with a coverageData >= 14X There is a 1.16% of reference with a coverageData >= 15X There is a 1.12% of reference with a coverageData >= 16X There is a 1.09% of reference with a coverageData >= 17X There is a 1.05% of reference with a coverageData >= 18X There is a 1.02% of reference with a coverageData >= 19X There is a 0.99% of reference with a coverageData >= 20X There is a 0.96% of reference with a coverageData >= 21X There is a 0.94% of reference with a coverageData >= 22X There is a 0.91% of reference with a coverageData >= 23X There is a 0.89% of reference with a coverageData >= 24X There is a 0.87% of reference with a coverageData >= 25X There is a 0.85% of reference with a coverageData >= 26X There is a 0.83% of reference with a coverageData >= 27X There is a 0.81% of reference with a coverageData >= 28X There is a 0.79% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.76% of reference with a coverageData >= 31X There is a 0.74% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.71% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.68% of reference with a coverageData >= 36X There is a 0.67% of reference with a coverageData >= 37X There is a 0.66% of reference with a coverageData >= 38X There is a 0.65% of reference with a coverageData >= 39X There is a 0.63% of reference with a coverageData >= 40X There is a 0.62% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.6% of reference with a coverageData >= 43X There is a 0.59% of reference with a coverageData >= 44X There is a 0.58% of reference with a coverageData >= 45X There is a 0.57% of reference with a coverageData >= 46X There is a 0.56% of reference with a coverageData >= 47X There is a 0.55% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 333093733 1.3363807546942883 33.814511125686835 chr2 243199373 539121696 2.2167890046328367 68.31415604920407 chr3 198022430 288547198 1.4571440114132526 25.918861048501185 chr4 191154276 343308969 1.7959784954012747 85.9814995499624 chr5 180915260 306611892 1.6947818111086925 28.77706985277372 chr6 171115067 349092271 2.040102470929693 28.499547269432238 chr7 159138663 221957333 1.3947417228206824 23.326308701311017 chr8 146364022 173202301 1.183366640471249 22.93347138614548 chr9 141213431 185642141 1.314620993806177 26.636705589233124 chr10 135534747 135379393 0.9988537699487497 31.884083356057207 chr11 135006516 161826469 1.1986567300203494 21.21977601406994 chr12 133851895 185675584 1.3871718738087346 22.89650362975099 chr13 115169878 137277985 1.1919608441366933 24.48086614725177 chr14 107349540 83650212 0.7792321420287409 13.345606942249944 chr15 102531392 151881038 1.4813125525497597 22.720194357406317 chr16 90354753 54396862 0.6020365303859555 16.882065947026536 chr17 81195210 86279870 1.062622659637188 15.31556257737758 chr18 78077248 138242014 1.7705800030246968 25.846288467156008 chr19 59128983 25573988 0.4325118867679493 13.708731852434111 chr20 63025520 56612410 0.8982458216925461 26.493676964924777 chr21 48129895 61793899 1.2838984793131172 45.36772036821401 chr22 51304566 29600482 0.5769560939273904 38.531409882795415 chrMT 16571 141213366 8521.71661336069 7064.205172290758 chrX 155270560 94716989 0.6100125419783377 14.927757840665272 chrY 59373566 21797838 0.36713034888286816 9.247844184568617