BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472717.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 = 17,407,296 number of mapped reads = 17,170,728 (98.64%) number of supplementary alignments = 62,538 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,628,210 number of mapped paired reads (second in pair) = 8,542,518 number of mapped paired reads (both in pair) = 17,044,884 number of mapped paired reads (singletons) = 125,844 number of mapped bases = 1,688,805,032 bp number of sequenced bases = 1,688,567,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,719,494 duplication rate = 46.8% >>>>>>> Insert size mean insert size = 25,473.1584 std insert size = 1,593,380.2575 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 55.1074 >>>>>>> ACTG content number of A's = 467,993,812 bp (27.72%) number of C's = 379,179,108 bp (22.46%) number of T's = 464,568,708 bp (27.51%) number of G's = 376,499,132 bp (22.3%) number of N's = 326,924 bp (0.02%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,805,940 number of insertions = 102,955 mapped reads with insertion percentage = 0.59% number of deletions = 96,740 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.5455X std coverageData = 17.7463X There is a 5.06% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 160505962 0.6439541107502396 17.942611297174395 chr2 243199373 136366274 0.5607180327722309 23.6684437552213 chr3 198022430 185525729 0.9368924974812197 20.58220360611619 chr4 191154276 83502865 0.43683493117360345 17.713285129452906 chr5 180915260 85780106 0.47414522135943643 15.371694841401363 chr6 171115067 120121906 0.7019949096592412 20.079273784233802 chr7 159138663 93987792 0.5906031270351945 21.378189874212453 chr8 146364022 59322850 0.40531032961092034 10.82460645035091 chr9 141213431 111773598 0.7915224296193186 21.105769705229513 chr10 135534747 57580844 0.4248419337072286 20.429995484936693 chr11 135006516 77351143 0.5729437755433967 20.362401260667614 chr12 133851895 85950404 0.6421306474592683 17.68024055381913 chr13 115169878 28976650 0.25159920721631746 8.084205932303972 chr14 107349540 29338925 0.27330275472070026 12.96576933014742 chr15 102531392 31099995 0.30332168902963885 10.015605966070362 chr16 90354753 69793853 0.7724425188788906 22.326259369024836 chr17 81195210 54860924 0.6756670005533577 15.797176580533705 chr18 78077248 26480588 0.33915882895872557 10.306000895172662 chr19 59128983 37369602 0.6320014332057766 16.543548658330884 chr20 63025520 34960612 0.5547056493940867 13.799311575844479 chr21 48129895 10239181 0.21274056384290888 9.423020275882665 chr22 51304566 19020301 0.370733103950241 11.945784050455698 chrMT 16571 8345 0.5035906101019854 1.7175230378019517 chrX 155270560 85915591 0.5533282742072934 17.216946183028305 chrY 59373566 2970992 0.050038968520098655 2.2633396028870343