BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006448.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,115,082 number of mapped reads = 1,995,361 (94.34%) number of supplementary alignments = 6,872 (0.32%) number of secondary alignments = 0 number of mapped bases = 111,364,199 bp number of sequenced bases = 111,331,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,579 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.443 >>>>>>> ACTG content number of A's = 31,637,900 bp (28.42%) number of C's = 23,331,356 bp (20.96%) number of T's = 32,054,701 bp (28.79%) number of G's = 24,305,673 bp (21.83%) number of N's = 2,338 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 453,343 number of insertions = 7,167 mapped reads with insertion percentage = 0.36% number of deletions = 19,444 mapped reads with deletion percentage = 0.97% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.2897X There is a 3.25% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 9239025 0.03706720955371261 0.3880520353363088 chr2 243199373 9294277 0.038216698034003564 0.2545483854108042 chr3 198022430 7535332 0.038052921580651246 0.20908129152800134 chr4 191154276 7344531 0.038422007363308995 0.2251495745032692 chr5 180915260 6807406 0.037627594267061824 0.2078550631928452 chr6 171115067 6366403 0.03720539115354465 0.21773010556581768 chr7 159138663 6215867 0.03905943962844529 0.2878730939730895 chr8 146364022 5686086 0.03884893242411718 0.7121205307830832 chr9 141213431 4628974 0.03277998393793009 0.22321971337610524 chr10 135534747 5508883 0.040645540143296244 0.2944328042677203 chr11 135006516 5193743 0.038470313536570336 0.23788646014022824 chr12 133851895 5185464 0.03874031069937411 0.21300004133807376 chr13 115169878 3595735 0.0312211410000799 0.1888579210436378 chr14 107349540 3410587 0.03177085807726796 0.2005250141197769 chr15 102531392 3325878 0.03243765577668155 0.19348179847786828 chr16 90354753 3328538 0.03683854904677787 0.23555059352410487 chr17 81195210 3139054 0.03866058108600249 0.23121049947162164 chr18 78077248 2873105 0.03679823602389264 0.33140305164745715 chr19 59128983 2328160 0.03937426084260573 0.3240049569604959 chr20 63025520 2403578 0.03813658340304055 0.2130029808596973 chr21 48129895 2106931 0.043775931777952144 0.2465044764247558 chr22 51304566 1418190 0.02764256888948247 0.1945558733858123 chrMT 16571 86642 5.228531772373423 3.458200052582072 chrX 155270560 3318347 0.02137138553502995 0.16255983499024132 chrY 59373566 1023463 0.017237687896327465 0.23696350377298783