BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472564.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 226,744 number of mapped reads = 194,730 (85.88%) number of supplementary alignments = 864 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 99,668 number of mapped paired reads (second in pair) = 95,062 number of mapped paired reads (both in pair) = 189,386 number of mapped paired reads (singletons) = 5,344 number of mapped bases = 19,101,725 bp number of sequenced bases = 19,099,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,672 duplication rate = 12.5% >>>>>>> Insert size mean insert size = 29,412.3367 std insert size = 1,628,132.8923 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.3208 >>>>>>> ACTG content number of A's = 5,298,822 bp (27.74%) number of C's = 4,287,282 bp (22.45%) number of T's = 5,249,954 bp (27.49%) number of G's = 4,260,742 bp (22.31%) number of N's = 2,702 bp (0.01%) GC percentage = 44.76% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 119,707 number of insertions = 1,117 mapped reads with insertion percentage = 0.56% number of deletions = 982 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.0062X std coverageData = 0.1599X There is a 0.28% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 1982953 0.007955659215789878 0.20765833617657728 chr2 243199373 1385053 0.005695133926188206 0.15815945446497578 chr3 198022430 2167302 0.010944729847017835 0.20231000247564565 chr4 191154276 780771 0.0040845071129876264 0.13086958948450225 chr5 180915260 1037699 0.005735829028463381 0.14875825234230697 chr6 171115067 1242563 0.007261563939311083 0.16492038879717177 chr7 159138663 816518 0.0051308587404683675 0.13735609116278535 chr8 146364022 881795 0.006024670461706771 0.154972247338079 chr9 141213431 1162213 0.008230187396268277 0.18063358589362072 chr10 135534747 522468 0.003854863874870405 0.1316781100383674 chr11 135006516 838806 0.006213077893218131 0.16172981649522214 chr12 133851895 1006172 0.007517054577374493 0.18489704509295454 chr13 115169878 466362 0.004049340054002662 0.12750832874647577 chr14 107349540 514917 0.004796639091327266 0.1512970270701531 chr15 102531392 499240 0.004869142906008727 0.13921038548827946 chr16 90354753 626259 0.006931112965357783 0.1676960742113016 chr17 81195210 690304 0.008501782309572202 0.17418330218311165 chr18 78077248 334293 0.004281567403605209 0.13874432562668465 chr19 59128983 387280 0.006549749046081175 0.15696226221567872 chr20 63025520 402520 0.006386619261530884 0.1616915860220819 chr21 48129895 85000 0.001766054133299065 0.07179461278068684 chr22 51304566 179664 0.0035019105317058916 0.10001230319562218 chrMT 16571 2166 0.13071027698992216 0.46329791111214863 chrX 155270560 1051889 0.006774555331029913 0.1584610452960594 chrY 59373566 37518 6.318973665822936E-4 0.03697880182929116