BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085038.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,177,721 number of mapped reads = 2,848,556 (89.64%) number of supplementary alignments = 28,801 (0.91%) number of secondary alignments = 0 number of mapped bases = 188,051,528 bp number of sequenced bases = 187,975,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,198 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9228 >>>>>>> ACTG content number of A's = 53,395,538 bp (28.41%) number of C's = 35,298,218 bp (18.78%) number of T's = 57,665,553 bp (30.68%) number of G's = 41,590,118 bp (22.13%) number of N's = 25,753 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,612,867 number of insertions = 15,446 mapped reads with insertion percentage = 0.54% number of deletions = 47,094 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.5199X There is a 5.15% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14936569 0.05992590485862822 0.9495803655458364 chr2 243199373 16226077 0.06671923862237918 0.6090409314222393 chr3 198022430 12686885 0.06406791897261335 0.2953913796467649 chr4 191154276 12537197 0.06558679859193943 0.30665410574110763 chr5 180915260 11988197 0.06626415593687343 0.295591693557336 chr6 171115067 11016084 0.06437822333903537 0.4042556868783995 chr7 159138663 10378672 0.06521779060064116 0.4991313483843751 chr8 146364022 9688176 0.06619233242989182 0.8385487779294332 chr9 141213431 7940708 0.056231959975535185 0.4806255794887344 chr10 135534747 8693513 0.06414231916484117 0.5766411352508524 chr11 135006516 8663046 0.06416761395427759 0.530416530764625 chr12 133851895 8661055 0.0647062561198704 0.29848142366177555 chr13 115169878 6182094 0.053678045921000284 0.26121972596648996 chr14 107349540 5554991 0.051746761094644655 0.3107760096426487 chr15 102531392 5046340 0.04921751184261694 0.2588388516174501 chr16 90354753 5039145 0.05577066875496854 0.32345017604750315 chr17 81195210 4687013 0.057725240195819434 0.34166064646759037 chr18 78077248 4830123 0.061863386885767285 0.925013908597519 chr19 59128983 3405174 0.057588915405495815 0.673452222354373 chr20 63025520 3529386 0.05599931583269761 0.2863502239965786 chr21 48129895 2418800 0.050255667501456214 0.2809987563216847 chr22 51304566 1864419 0.03634021580067552 0.21511832579791543 chrMT 16571 30777 1.8572807917446141 1.77307381273234 chrX 155270560 11578192 0.07456785111098975 0.3765249408240401 chrY 59373566 468895 0.007897369681315755 0.1463547517255244