BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818858.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 = 1,356,935 number of mapped reads = 1,262,952 (93.07%) number of supplementary alignments = 21,245 (1.57%) number of secondary alignments = 0 number of mapped bases = 116,810,401 bp number of sequenced bases = 116,733,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,857 duplication rate = 17.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3767 >>>>>>> ACTG content number of A's = 33,243,094 bp (28.48%) number of C's = 25,953,625 bp (22.23%) number of T's = 33,679,421 bp (28.85%) number of G's = 23,855,932 bp (20.44%) number of N's = 1,560 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 728,992 number of insertions = 17,051 mapped reads with insertion percentage = 1.31% number of deletions = 39,115 mapped reads with deletion percentage = 3.02% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.4537X There is a 2.71% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 9489639 0.03807267946586179 0.6202342437052908 chr2 243199373 8933563 0.03673349519696336 0.6994245422216734 chr3 198022430 7351357 0.03712386016068988 0.2509686827626452 chr4 191154276 6060150 0.03170292669780508 0.30540792229163505 chr5 180915260 5199921 0.028742301782613583 0.23367618234091309 chr6 171115067 5958469 0.03482141639812466 0.26163285705275646 chr7 159138663 9787281 0.06150159122550879 0.8987807972977058 chr8 146364022 10441234 0.07133743564384969 0.4282693573984651 chr9 141213431 4470028 0.031654411116177755 0.38740205752982754 chr10 135534747 5527541 0.0407832022588274 0.5917163730235822 chr11 135006516 5351007 0.03963517583106878 0.30777197188998107 chr12 133851895 4666270 0.03486144144615958 0.24348266848133443 chr13 115169878 3682685 0.03197611271238822 0.22906449681954716 chr14 107349540 3563535 0.03319562431287549 0.25258317717869 chr15 102531392 3400832 0.033168690424099576 0.23635230979482336 chr16 90354753 2968963 0.03285895762450925 0.4990605683208004 chr17 81195210 2871070 0.03536009082309166 0.29926455022360404 chr18 78077248 2346884 0.03005848771719003 0.4314325808066856 chr19 59128983 2100073 0.035516812457268204 0.5247784766181536 chr20 63025520 4904840 0.07782307865131458 0.3909522200711742 chr21 48129895 1172865 0.024368742130021267 0.24686845672460112 chr22 51304566 1093229 0.02130861023168971 0.20891342293622633 chrMT 16571 106243 6.41138132882747 5.057935538716512 chrX 155270560 4922399 0.031702075396649564 0.26540493636090123 chrY 59373566 440323 0.007416145427411249 0.5689735623799885