BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617368.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,695,589 (95.92%) number of supplementary alignments = 98,476 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,447,569 number of mapped paired reads (second in pair) = 15,248,020 number of mapped paired reads (both in pair) = 30,153,118 number of mapped paired reads (singletons) = 542,471 number of mapped bases = 3,012,356,823 bp number of sequenced bases = 3,011,450,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,635,871 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 71,128.3529 std insert size = 2,553,597.9646 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.4402 >>>>>>> ACTG content number of A's = 909,411,139 bp (30.2%) number of C's = 599,719,514 bp (19.91%) number of T's = 899,367,556 bp (29.86%) number of G's = 601,769,898 bp (19.98%) number of N's = 1,182,868 bp (0.04%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 26,000,366 number of insertions = 308,385 mapped reads with insertion percentage = 0.97% number of deletions = 374,971 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 0.9731X std coverageData = 9.9156X There is a 53.67% of reference with a coverageData >= 1X There is a 24.42% of reference with a coverageData >= 2X There is a 9.43% of reference with a coverageData >= 3X There is a 3.31% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196057906 0.7865894384271163 20.036844935358523 chr2 243199373 297173170 1.2219323032547456 9.010698949990973 chr3 198022430 239127446 1.207577575934201 1.4920369505645017 chr4 191154276 164007091 0.8579828525520402 9.653254742011665 chr5 180915260 188584258 1.04239000071083 1.4794165313318512 chr6 171115067 140592990 0.8216283490687585 3.730107824419158 chr7 159138663 244062408 1.5336462139310545 10.95393923517984 chr8 146364022 126581987 0.8648435952381796 7.708670394659372 chr9 141213431 126786778 0.8978379542382198 15.287908578779227 chr10 135534747 126904935 0.9363276783923167 20.275375471198625 chr11 135006516 161734652 1.1979766369202505 5.663836237097742 chr12 133851895 132839589 0.992437118652672 1.4055735405309344 chr13 115169878 130707576 1.13491112667498 1.3409259053608962 chr14 107349540 87207088 0.8123657353352423 1.3976057312409016 chr15 102531392 67836407 0.6616159761100289 1.103726536263483 chr16 90354753 76205592 0.8434043530615374 7.866108990706598 chr17 81195210 95039614 1.1705076444780425 7.318261595594613 chr18 78077248 54534861 0.6984731454674222 15.69144807817165 chr19 59128983 56897989 0.9622690280331728 9.587968271478754 chr20 63025520 87061261 1.3813652152334484 2.4659391089805447 chr21 48129895 47963944 0.9965520182414692 3.302769268128879 chr22 51304566 27310128 0.5323137905503381 0.9434471358319209 chrMT 16571 2112083 127.4565807736407 19.586639712909367 chrX 155270560 124615839 0.8025722261837659 3.054031408870412 chrY 59373566 10411231 0.17535128343141795 8.614298122722602