BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819139.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 = 787,078 number of mapped reads = 717,835 (91.2%) number of supplementary alignments = 2,445 (0.31%) number of secondary alignments = 0 number of mapped bases = 41,566,864 bp number of sequenced bases = 41,554,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,617 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5411 >>>>>>> ACTG content number of A's = 10,167,034 bp (24.47%) number of C's = 7,150,421 bp (17.21%) number of T's = 13,258,609 bp (31.91%) number of G's = 10,978,310 bp (26.42%) number of N's = 551 bp (0%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 209,225 number of insertions = 2,746 mapped reads with insertion percentage = 0.38% number of deletions = 7,085 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0134X std coverageData = 0.1517X There is a 1.24% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3995516 0.01603011452476983 0.24073542508761075 chr2 243199373 3250027 0.013363632314956667 0.17135295327808717 chr3 198022430 2206378 0.011142061028137066 0.11197782335576807 chr4 191154276 2260932 0.011827786682626969 0.13058919363114294 chr5 180915260 2350668 0.012993199136435478 0.12063187829689145 chr6 171115067 1797712 0.010505866207561956 0.12287689527724711 chr7 159138663 2081865 0.013082081756587335 0.17882853222861908 chr8 146364022 3819792 0.02609788900171109 0.18085771936244938 chr9 141213431 1711746 0.01212169400515451 0.12770558455671002 chr10 135534747 2246345 0.01657394173613649 0.17946212489162364 chr11 135006516 1298654 0.009619194972781906 0.12252409624304332 chr12 133851895 1929885 0.014418062590746288 0.1268562475043225 chr13 115169878 859086 0.0074592941741242445 0.09087674220629442 chr14 107349540 1009721 0.009405918274079238 0.10348949085616829 chr15 102531392 1138577 0.011104667339345203 0.11139824427761551 chr16 90354753 1257954 0.013922388786785794 0.13064608028907 chr17 81195210 1545193 0.019030593060846816 0.1495014645266703 chr18 78077248 930131 0.011912958305087802 0.1912446297722832 chr19 59128983 948844 0.016047020460338377 0.18225092481181943 chr20 63025520 1238877 0.01965675174119944 0.1509705412090595 chr21 48129895 607221 0.01261629596324696 0.12922965970944772 chr22 51304566 363729 0.00708960290201071 0.08953323460390908 chrMT 16571 6288 0.3794580894333474 0.6500222326135608 chrX 155270560 2553471 0.0164453003840522 0.14117944980497232 chrY 59373566 158252 0.0026653612147870655 0.0980317931429612