BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,560,161 number of mapped reads = 1,431,009 (91.72%) number of supplementary alignments = 5,870 (0.38%) number of secondary alignments = 0 number of mapped bases = 83,859,714 bp number of sequenced bases = 83,833,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,115 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1325 >>>>>>> ACTG content number of A's = 21,360,491 bp (25.48%) number of C's = 17,323,887 bp (20.66%) number of T's = 25,310,190 bp (30.19%) number of G's = 19,837,471 bp (23.66%) number of N's = 1,217 bp (0%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 426,771 number of insertions = 4,617 mapped reads with insertion percentage = 0.32% number of deletions = 15,752 mapped reads with deletion percentage = 1.09% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.259X There is a 2.4% of reference with a coverageData >= 1X There is a 0.22% 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 8351258 0.03350546516792831 0.4637659798546574 chr2 243199373 6419038 0.02639413877107323 0.28514789602431123 chr3 198022430 4563952 0.023047651723090156 0.16755840404475625 chr4 191154276 4707709 0.02462779854320392 0.20001646151608077 chr5 180915260 4569577 0.025258107027566385 0.1747128342233474 chr6 171115067 3481963 0.02034866397825739 0.19417539347805218 chr7 159138663 4138042 0.026002744537322146 0.3179190589879777 chr8 146364022 7463787 0.050994683652516734 0.29799235124684426 chr9 141213431 3429685 0.024287243612117888 0.22603852937784943 chr10 135534747 4367031 0.03222074852878871 0.26117117743118334 chr11 135006516 2855696 0.0211522827535228 0.2277313977513693 chr12 133851895 3788201 0.02830143719668668 0.18644982003293822 chr13 115169878 1828663 0.015877962465150827 0.1386868796800842 chr14 107349540 1990692 0.018544019843960206 0.1534877108782313 chr15 102531392 2291355 0.02234783860146949 0.16662636266129685 chr16 90354753 2691150 0.02978426602527484 0.19965057342236375 chr17 81195210 3021082 0.037207638233831775 0.22388376995388676 chr18 78077248 1974942 0.025294718379418293 0.44194848523081975 chr19 59128983 1790022 0.03027317415555752 0.3072822326054822 chr20 63025520 2460657 0.039042232416329134 0.22243531357603333 chr21 48129895 1574403 0.032711540301511154 0.2197118692884171 chr22 51304566 709421 0.013827638655007822 0.12896877670708398 chrMT 16571 56667 3.4196487840202763 2.697525672874313 chrX 155270560 5034483 0.03242393793131164 0.21811152051063284 chrY 59373566 300238 0.005056762128789772 0.16388693981342278