BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054632.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,300,816 number of mapped reads = 6,405,797 (68.87%) number of supplementary alignments = 173 (0%) number of secondary alignments = 0 number of mapped bases = 301,516,784 bp number of sequenced bases = 301,452,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,592,130 duplication rate = 17.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.413 >>>>>>> ACTG content number of A's = 92,600,446 bp (30.72%) number of C's = 56,462,397 bp (18.73%) number of T's = 92,444,581 bp (30.67%) number of G's = 59,550,527 bp (19.75%) number of N's = 394,679 bp (0.13%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,485,998 number of insertions = 14,505 mapped reads with insertion percentage = 0.23% number of deletions = 43,764 mapped reads with deletion percentage = 0.68% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.0974X std coverageData = 0.8203X There is a 4.2% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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% 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 20082226 0.08057041510841412 0.8006201963679628 chr2 243199373 25226514 0.1037277098572125 0.9193996877805044 chr3 198022430 23894588 0.1206660679802788 0.8630886022076028 chr4 191154276 19781982 0.1034869970682738 0.8420827698348526 chr5 180915260 18317302 0.10124796548395089 0.7664297317971318 chr6 171115067 17167042 0.10032454944484813 0.8305170032153565 chr7 159138663 15974004 0.10037789496823911 0.8785235085033023 chr8 146364022 18854220 0.12881731276829766 0.9502046301615233 chr9 141213431 11916308 0.08438508940413748 0.7340034435371173 chr10 135534747 11788697 0.0869791493394679 0.7480212395407824 chr11 135006516 16048418 0.11887143284254517 0.8906448270573153 chr12 133851895 15509679 0.11587194189518199 1.004881641506511 chr13 115169878 11126145 0.09660638001196806 0.7457523319116262 chr14 107349540 6561323 0.06112110960140118 0.6344418088576732 chr15 102531392 8775695 0.08559032340066153 0.7081307888441131 chr16 90354753 9430510 0.10437204116976558 0.8147172043218082 chr17 81195210 6221733 0.07662684781528369 0.6313053020201376 chr18 78077248 11280260 0.14447563520681467 1.0495603106894382 chr19 59128983 5673155 0.09594541817166041 0.8318167036815537 chr20 63025520 6058279 0.09612422079183162 0.7547489198074988 chr21 48129895 3667978 0.07620997303235338 0.7118964446406858 chr22 51304566 3286035 0.06404956237228476 0.5805338610252943 chrMT 16571 22146 1.3364311145977914 3.5973776358025416 chrX 155270560 14222706 0.09159950218508904 0.8023290234724892 chrY 59373566 629839 0.010608070938504856 0.25591744042118886