BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818752.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 = 1,647,534 number of mapped reads = 1,359,507 (82.52%) number of supplementary alignments = 9,922 (0.6%) number of secondary alignments = 0 number of mapped bases = 92,347,093 bp number of sequenced bases = 92,305,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 451,267 duplication rate = 29.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2283 >>>>>>> ACTG content number of A's = 26,835,676 bp (29.07%) number of C's = 19,347,878 bp (20.96%) number of T's = 26,932,222 bp (29.18%) number of G's = 19,183,744 bp (20.78%) number of N's = 5,913 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 487,602 number of insertions = 11,158 mapped reads with insertion percentage = 0.81% number of deletions = 25,344 mapped reads with deletion percentage = 1.85% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.4068X There is a 1.78% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7614314 0.030548826596504246 0.562077251687316 chr2 243199373 8203556 0.03373181393851702 0.7315680097072828 chr3 198022430 6256159 0.03159318366106304 0.2711781570237382 chr4 191154276 6001396 0.03139556239903313 0.3251412326566563 chr5 180915260 5807100 0.03209845316531065 0.29031875383651173 chr6 171115067 5456666 0.0318888692601219 0.318072708808599 chr7 159138663 5135721 0.032271987857532776 0.36408215138077227 chr8 146364022 4772311 0.03260576564369077 0.3128392571077521 chr9 141213431 4024046 0.028496198778712487 0.3160405635448109 chr10 135534747 4447806 0.03281672116154834 0.4530654847504825 chr11 135006516 4259231 0.03154833652621626 0.30255450640922615 chr12 133851895 4253428 0.031777122019826465 0.2990076714852347 chr13 115169878 2863455 0.024862881247473406 0.24164402927919823 chr14 107349540 2827915 0.02634305652357709 0.2882069600354006 chr15 102531392 2644881 0.025795816758247075 0.24467648288516874 chr16 90354753 2731660 0.03023260989933756 0.5126360712251302 chr17 81195210 2404900 0.02961874228787634 0.27880339361751105 chr18 78077248 2500045 0.03202014753388849 0.3978259523097274 chr19 59128983 1847042 0.03123750665557701 0.4552330943978115 chr20 63025520 1980941 0.031430775977730925 0.2938723128034852 chr21 48129895 1262216 0.026225197457837794 0.26765439746292075 chr22 51304566 1084618 0.021140769420016144 0.2616379335756778 chrMT 16571 98987 5.9735079355500575 6.029300723321726 chrX 155270560 2975017 0.01916021298564261 0.2567733996397269 chrY 59373566 893682 0.01505184984172923 0.7579246148493591