BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472454.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 = 16,173,782 number of mapped reads = 16,004,664 (98.95%) number of supplementary alignments = 60,146 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,030,351 number of mapped paired reads (second in pair) = 7,974,313 number of mapped paired reads (both in pair) = 15,925,670 number of mapped paired reads (singletons) = 78,994 number of mapped bases = 1,567,055,419 bp number of sequenced bases = 1,566,861,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,000,196 duplication rate = 47.1% >>>>>>> Insert size mean insert size = 16,142.471 std insert size = 1,254,434.3905 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 55.1427 >>>>>>> ACTG content number of A's = 417,975,016 bp (26.68%) number of C's = 365,712,634 bp (23.34%) number of T's = 420,475,411 bp (26.84%) number of G's = 362,475,500 bp (23.13%) number of N's = 222,860 bp (0.01%) GC percentage = 46.47% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 7,172,114 number of insertions = 98,861 mapped reads with insertion percentage = 0.61% number of deletions = 78,995 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.5062X std coverageData = 16.7666X There is a 4.47% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 184926864 0.7419314072641768 22.098742936681884 chr2 243199373 127043114 0.5223825720965161 17.78392086959808 chr3 198022430 131066864 0.6618788790744564 14.77127868290062 chr4 191154276 59315988 0.31030426962565044 13.28067116909097 chr5 180915260 76551890 0.4231367215789315 16.746456254716204 chr6 171115067 104936496 0.6132510587159458 15.55565125095883 chr7 159138663 97835011 0.6147783898372955 22.646931063388948 chr8 146364022 82875147 0.5662262205393618 14.798322536259576 chr9 141213431 54088618 0.3830274331341755 9.437745014329613 chr10 135534747 43534618 0.3212063250466687 12.64486992606788 chr11 135006516 86821481 0.6430910416205393 23.3232034744293 chr12 133851895 73577121 0.5496905441645036 16.988288867017534 chr13 115169878 26545156 0.2304869681289408 7.70780311521931 chr14 107349540 32500548 0.3027544226086111 8.711092126991579 chr15 102531392 48499346 0.473019482657565 20.14197969819876 chr16 90354753 90280761 0.9991810945462936 28.60638754537709 chr17 81195210 75446423 0.9291979539187102 22.78560621758699 chr18 78077248 22424363 0.2872073949122797 9.879244895722744 chr19 59128983 35951708 0.6080217547458917 13.061859141947105 chr20 63025520 28387514 0.4504130073024388 13.652021914764223 chr21 48129895 15008165 0.31182625684099247 21.659547047004413 chr22 51304566 20682217 0.40312624416314136 11.54391212655293 chrMT 16571 9072 0.5474624343733028 0.9552637640274688 chrX 155270560 46118474 0.2970200790156228 8.11990878842708 chrY 59373566 2628460 0.044269869187240664 3.3302684885891307