BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365331.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 160,488,970 number of mapped reads = 157,080,523 (97.88%) number of supplementary alignments = 1,235,900 (0.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 78,876,693 number of mapped paired reads (second in pair) = 78,203,830 number of mapped paired reads (both in pair) = 156,192,754 number of mapped paired reads (singletons) = 887,769 number of mapped bases = 20,676,853,304 bp number of sequenced bases = 20,669,368,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,721,542 duplication rate = 33.93% >>>>>>> Insert size mean insert size = 76,949.5692 std insert size = 2,749,736.9099 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 54.28 >>>>>>> ACTG content number of A's = 6,149,225,971 bp (29.75%) number of C's = 4,119,621,801 bp (19.93%) number of T's = 6,066,228,405 bp (29.35%) number of G's = 4,333,077,440 bp (20.96%) number of N's = 1,214,857 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 142,310,443 number of insertions = 6,315,413 mapped reads with insertion percentage = 3.9% number of deletions = 3,094,849 mapped reads with deletion percentage = 1.91% homopolymer indels = 50.72% >>>>>>> Coverage mean coverageData = 6.6792X std coverageData = 55.1542X There is a 79% of reference with a coverageData >= 1X There is a 73.06% of reference with a coverageData >= 2X There is a 65.2% of reference with a coverageData >= 3X There is a 58.84% of reference with a coverageData >= 4X There is a 51.83% of reference with a coverageData >= 5X There is a 45.93% of reference with a coverageData >= 6X There is a 39.99% of reference with a coverageData >= 7X There is a 34.96% of reference with a coverageData >= 8X There is a 30.13% of reference with a coverageData >= 9X There is a 26.04% of reference with a coverageData >= 10X There is a 22.26% of reference with a coverageData >= 11X There is a 19.06% of reference with a coverageData >= 12X There is a 16.18% of reference with a coverageData >= 13X There is a 13.75% of reference with a coverageData >= 14X There is a 11.6% of reference with a coverageData >= 15X There is a 9.8% of reference with a coverageData >= 16X There is a 8.22% of reference with a coverageData >= 17X There is a 6.91% of reference with a coverageData >= 18X There is a 5.78% of reference with a coverageData >= 19X There is a 4.85% of reference with a coverageData >= 20X There is a 4.04% of reference with a coverageData >= 21X There is a 3.38% of reference with a coverageData >= 22X There is a 2.81% of reference with a coverageData >= 23X There is a 2.35% of reference with a coverageData >= 24X There is a 1.96% of reference with a coverageData >= 25X There is a 1.64% of reference with a coverageData >= 26X There is a 1.37% of reference with a coverageData >= 27X There is a 1.15% of reference with a coverageData >= 28X There is a 0.96% of reference with a coverageData >= 29X There is a 0.81% of reference with a coverageData >= 30X There is a 0.68% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.49% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1780913161 7.145070105963748 153.47936931937377 chr2 243199373 1848234068 7.599666254073772 36.170462244088625 chr3 198022430 1403496748 7.087564514787542 7.565204896508896 chr4 191154276 1374382311 7.189911414798798 25.42116638011405 chr5 180915260 1318829766 7.289765197253123 7.838601952564009 chr6 171115067 1251858686 7.315888121061835 33.462428825561126 chr7 159138663 1142030828 7.176325391146462 26.20480805505958 chr8 146364022 1046045543 7.1468761838206385 19.251258435898183 chr9 141213431 868828721 6.152592673709628 49.02419262742715 chr10 135534747 1050340914 7.74960618770329 84.53521582622477 chr11 135006516 955321427 7.07611347440445 44.38868274215652 chr12 133851895 987656497 7.378726292967313 39.07435561855027 chr13 115169878 663165436 5.758150025998986 6.537079393898392 chr14 107349540 629418043 5.863257942232449 7.003571092805877 chr15 102531392 619468556 6.041745302745914 18.528866530106868 chr16 90354753 583724740 6.460365621275065 15.339030527266486 chr17 81195210 605317807 7.455092572579097 36.36806716143641 chr18 78077248 547341165 7.010251757336529 48.62589903015522 chr19 59128983 383040190 6.4780446164616095 79.04000474201037 chr20 63025520 424683566 6.738279446167203 11.503456263170879 chr21 48129895 269680898 5.603188995114159 19.924037626820898 chr22 51304566 258733200 5.043083299837289 17.297384429817455 chrMT 16571 11995093 723.8605394967111 170.67413143145228 chrX 155270560 515008693 3.316847012080075 14.020796017603136 chrY 59373566 137337247 2.3131042356458766 47.42765640145746