BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084795.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,866,618 number of mapped reads = 1,696,207 (90.87%) number of supplementary alignments = 18,256 (0.98%) number of secondary alignments = 0 number of mapped bases = 113,873,352 bp number of sequenced bases = 113,830,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,439 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7598 >>>>>>> ACTG content number of A's = 31,358,852 bp (27.55%) number of C's = 21,194,603 bp (18.62%) number of T's = 35,993,207 bp (31.62%) number of G's = 25,267,299 bp (22.2%) number of N's = 16,236 bp (0.01%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 829,696 number of insertions = 9,010 mapped reads with insertion percentage = 0.53% number of deletions = 26,321 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.2587X There is a 2.98% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 9436525 0.03785958471092435 0.2795640789163291 chr2 243199373 12031434 0.04947148445156559 0.4062563188743114 chr3 198022430 7649386 0.038628886636731 0.23710759985393326 chr4 191154276 6051291 0.03165658193280489 0.214730047756304 chr5 180915260 6466694 0.035744325824145516 0.22772465614181173 chr6 171115067 6121841 0.035776165754006925 0.2406729855270207 chr7 159138663 5565608 0.03497332386159358 0.23166088499012433 chr8 146364022 7265572 0.04964042324554323 0.2938892564723969 chr9 141213431 7919127 0.05607913456900569 0.31336149537217345 chr10 135534747 2815159 0.02077075482348449 0.179648657959633 chr11 135006516 5285645 0.03915103623591027 0.260971628644416 chr12 133851895 5235390 0.03911330504510228 0.2372697050051331 chr13 115169878 2267121 0.019685016945142547 0.17019458898447268 chr14 107349540 2850912 0.02655728194084483 0.19652998949846176 chr15 102531392 3058125 0.029826231170254666 0.20997678697391167 chr16 90354753 1775431 0.019649558446582217 0.1709403971663987 chr17 81195210 3023281 0.03723472111224295 0.23237681053845424 chr18 78077248 4163624 0.053326982016579275 0.3578631532952902 chr19 59128983 2222671 0.037590211893209796 0.25566285351014423 chr20 63025520 2492058 0.03954045916638212 0.2419038239624871 chr21 48129895 1342490 0.027893058981325432 0.2030787823069376 chr22 51304566 1060883 0.02067814003143502 0.16867232752093975 chrMT 16571 13852 0.8359181702975077 1.1008945003157702 chrX 155270560 7518645 0.048422862646982145 0.2699030008784128 chrY 59373566 240587 0.00405208944330546 0.08504273304639476