BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536759.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 23,342,018 number of mapped reads = 22,806,735 (97.71%) number of supplementary alignments = 613 (0%) number of secondary alignments = 0 number of mapped bases = 1,137,714,924 bp number of sequenced bases = 1,137,612,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,194 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6644 >>>>>>> ACTG content number of A's = 353,468,762 bp (31.07%) number of C's = 213,797,466 bp (18.79%) number of T's = 353,126,027 bp (31.04%) number of G's = 217,180,680 bp (19.09%) number of N's = 39,439 bp (0%) GC percentage = 37.88% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,139,731 number of insertions = 67,516 mapped reads with insertion percentage = 0.3% number of deletions = 61,453 mapped reads with deletion percentage = 0.27% homopolymer indels = 49.29% >>>>>>> Coverage mean coverageData = 0.3675X std coverageData = 0.7071X There is a 27.02% of reference with a coverageData >= 1X There is a 7.2% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.04% 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 89217299 0.3579421332715556 0.7124784591285678 chr2 243199373 102676321 0.4221899083596733 0.7472214419343726 chr3 198022430 85894248 0.4337601957515621 0.7486864289811702 chr4 191154276 94353171 0.493596967718368 0.8003603666848734 chr5 180915260 79216556 0.43786552886694025 0.7538382230840422 chr6 171115067 76602688 0.44766769719933547 0.7673599991164652 chr7 159138663 64617752 0.40604684481985376 0.7410291751468774 chr8 146364022 65309698 0.4462141522730224 0.762443143496631 chr9 141213431 49701761 0.3519619957396262 0.7005985557114107 chr10 135534747 48630976 0.3588081807538254 0.6859860168042842 chr11 135006516 49514376 0.3667554534923337 0.7103220606385676 chr12 133851895 55171541 0.41218348832491314 0.7493730132666083 chr13 115169878 45478462 0.39488156790441337 0.7308069218602747 chr14 107349540 37152897 0.3460927452507016 0.6971827637999648 chr15 102531392 30466078 0.2971390264554294 0.6508593465386824 chr16 90354753 21394780 0.236786436680315 0.5641612717073031 chr17 81195210 18374191 0.22629648965745638 0.5558774610687227 chr18 78077248 32766884 0.4196726298549867 0.7420319382572519 chr19 59128983 8961263 0.15155449232062726 0.439285915880919 chr20 63025520 17775362 0.2820343568763891 0.6240850091348141 chr21 48129895 14135497 0.29369474003631213 0.6553636896424822 chr22 51304566 6024512 0.11742642945269238 0.3907199389433371 chrMT 16571 1339 0.08080381389173857 0.2818942123268812 chrX 155270560 38684332 0.24914144703284383 0.5565703244304703 chrY 59373566 5592940 0.09419915926895818 0.3602848106404665