BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006052.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 = 9,966,024 number of mapped reads = 8,668,721 (86.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,407,650 number of mapped paired reads (second in pair) = 4,261,071 number of mapped paired reads (both in pair) = 7,923,736 number of mapped paired reads (singletons) = 744,985 number of mapped bases = 334,468,699 bp number of sequenced bases = 334,431,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 868,039 duplication rate = 9.08% >>>>>>> Insert size mean insert size = 72,759.2616 std insert size = 2,663,213.5328 median insert size = 98 >>>>>>> Mapping quality mean mapping quality = 46.1932 >>>>>>> ACTG content number of A's = 87,392,357 bp (26.13%) number of C's = 75,725,124 bp (22.64%) number of T's = 90,983,157 bp (27.21%) number of G's = 80,315,378 bp (24.02%) number of N's = 15,945 bp (0%) GC percentage = 46.66% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,597,275 number of insertions = 11,421 mapped reads with insertion percentage = 0.13% number of deletions = 28,805 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.108X std coverageData = 0.659X There is a 5.03% of reference with a coverageData >= 1X There is a 2.58% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 29117473 0.11682006200498092 0.6949387608558325 chr2 243199373 28822411 0.11851350866763953 0.7146543376168817 chr3 198022430 22323457 0.11273196172776993 0.6114652752856703 chr4 191154276 19873449 0.10396549538865665 0.6062953099403368 chr5 180915260 19796652 0.10942499820081512 0.6014642937131889 chr6 171115067 18845284 0.11013223049493356 0.6639801551804325 chr7 159138663 18325978 0.11515729524509076 0.75730265445734 chr8 146364022 16808761 0.1148421638754912 0.6998069998687445 chr9 141213431 14387988 0.10188824036149932 0.6084764434963398 chr10 135534747 16152053 0.11917278305023878 0.6522806957425165 chr11 135006516 15617385 0.11567874990567122 0.9063233753646341 chr12 133851895 15452644 0.1154458366091866 0.6248211241027934 chr13 115169878 9906220 0.08601398362165497 0.537262396090212 chr14 107349540 10296480 0.09591545525020415 0.5789753260720456 chr15 102531392 10365332 0.10109422878019642 0.589758021124165 chr16 90354753 10997209 0.1217114610451096 0.692871158640469 chr17 81195210 10768984 0.13263077957431232 0.7129623069891987 chr18 78077248 8533690 0.10929803775870789 0.6811830269382012 chr19 59128983 8324499 0.14078542497509217 0.8381082942391095 chr20 63025520 8147176 0.1292678902133612 0.6788031551498557 chr21 48129895 4375117 0.09090227601784712 0.6192567849538182 chr22 51304566 5075233 0.09892361237399416 0.6519463115947276 chrMT 16571 69751 4.2092209281274515 5.37381077163772 chrX 155270560 9934674 0.06398298557047775 0.46018721420927766 chrY 59373566 2150799 0.03622485804541368 0.35417797451555194