BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054570.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 = 12,971,268 number of mapped reads = 9,378,870 (72.3%) number of supplementary alignments = 288 (0%) number of secondary alignments = 0 number of mapped bases = 440,741,050 bp number of sequenced bases = 440,646,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,123,811 duplication rate = 21.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8385 >>>>>>> ACTG content number of A's = 134,695,213 bp (30.57%) number of C's = 86,104,071 bp (19.54%) number of T's = 130,958,973 bp (29.72%) number of G's = 88,830,493 bp (20.16%) number of N's = 57,640 bp (0.01%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,400,734 number of insertions = 20,386 mapped reads with insertion percentage = 0.22% number of deletions = 64,122 mapped reads with deletion percentage = 0.68% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.1424X std coverageData = 1.352X There is a 4.64% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 1.32% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 33648243 0.13499762955455183 1.3352902877401545 chr2 243199373 47775970 0.1964477515326489 1.6839918813638375 chr3 198022430 29070185 0.14680248596080758 1.320312206954626 chr4 191154276 21980481 0.11498817321774167 1.1488258076531 chr5 180915260 22537237 0.12457344394276082 1.1750478365597579 chr6 171115067 28201959 0.1648128332264277 1.5310336694294142 chr7 159138663 23044736 0.1448091592927358 1.4151941618902488 chr8 146364022 24810735 0.16951389187706253 1.5061920589437212 chr9 141213431 23063365 0.16332274371267136 1.4436389370385219 chr10 135534747 15172848 0.11194803056665609 1.135669496076094 chr11 135006516 21076136 0.1561119909204975 1.3986744539182598 chr12 133851895 23620490 0.17646735595338414 1.4834252136125863 chr13 115169878 12201432 0.1059429098292524 1.1103004108615222 chr14 107349540 8792921 0.081909256434634 1.1210426735755055 chr15 102531392 10815598 0.1054857228506173 1.0731866294165975 chr16 90354753 10429246 0.11542553826692438 1.1553156581598876 chr17 81195210 11053224 0.13613147869190806 1.286448788926775 chr18 78077248 14255407 0.18258080766371274 1.6003621426737151 chr19 59128983 8560090 0.1447697823586785 1.3401954777016456 chr20 63025520 9273209 0.14713419262546346 1.357107687029883 chr21 48129895 5014375 0.10418420817248822 1.145223826954633 chr22 51304566 5918042 0.11535117556593306 1.1238155195502075 chrMT 16571 31918 1.9261360207591576 4.7511039697231565 chrX 155270560 29381283 0.18922636074733035 1.5752889458268657 chrY 59373566 1011920 0.017043274779891104 0.37585965267338795