BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006015.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 = 8,544,380 number of mapped reads = 6,058,973 (70.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,050,272 number of mapped paired reads (second in pair) = 3,008,701 number of mapped paired reads (both in pair) = 5,375,120 number of mapped paired reads (singletons) = 683,853 number of mapped bases = 234,038,385 bp number of sequenced bases = 234,010,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,226 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 63,815.5499 std insert size = 2,422,813.0844 median insert size = 98 >>>>>>> Mapping quality mean mapping quality = 47.3452 >>>>>>> ACTG content number of A's = 68,076,918 bp (29.09%) number of C's = 48,705,189 bp (20.81%) number of T's = 67,661,667 bp (28.91%) number of G's = 49,386,701 bp (21.1%) number of N's = 180,015 bp (0.08%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,583,058 number of insertions = 6,740 mapped reads with insertion percentage = 0.11% number of deletions = 21,238 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0756X std coverageData = 0.4936X There is a 6% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 19180777 0.07695377818135908 0.690445601364132 chr2 243199373 20338101 0.08362727563446473 0.4178648361445782 chr3 198022430 16412217 0.08288059590017151 0.3435933766376573 chr4 191154276 15835608 0.08284202860311636 0.3818038343541244 chr5 180915260 14673253 0.08110566792430887 0.34052193293827276 chr6 171115067 13917373 0.08133341641972416 0.4182095588399048 chr7 159138663 12890526 0.08100184931175398 0.5409181641034286 chr8 146364022 11956537 0.08169041022936634 1.2454556540091293 chr9 141213431 9455791 0.06696098900110996 0.3540166109611133 chr10 135534747 10904533 0.08045562662982653 0.4865413065963668 chr11 135006516 10420872 0.07718791884089506 0.3769349026455536 chr12 133851895 10796998 0.08066376647114334 0.34072330203594986 chr13 115169878 7674546 0.06663674680631336 0.30718318504239567 chr14 107349540 7092137 0.06606583502826374 0.3235519561897882 chr15 102531392 6340731 0.06184185034764767 0.29590875380694215 chr16 90354753 6392588 0.07074988075060092 0.35836759806937185 chr17 81195210 5904667 0.07272186376511619 0.3343785743001229 chr18 78077248 6132874 0.07854879823633128 0.5195403902648181 chr19 59128983 4235829 0.07163710223123573 0.5640987918380624 chr20 63025520 4635555 0.07355044432794842 0.33377924465917946 chr21 48129895 2941873 0.061123611426952 0.33143393249047337 chr22 51304566 2399431 0.04676837145450173 0.26826035161420475 chrMT 16571 33958 2.0492426528272283 1.9483403477806935 chrX 155270560 12870556 0.08289115464000388 0.36941047691193857 chrY 59373566 601054 0.010123259229536592 0.23515249176431846