BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472808.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 1,941,234 number of mapped reads = 1,476,551 (76.06%) number of supplementary alignments = 14,690 (0.76%) number of secondary alignments = 0 number of mapped bases = 92,397,083 bp number of sequenced bases = 92,352,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,554 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7996 >>>>>>> ACTG content number of A's = 25,100,611 bp (27.18%) number of C's = 18,308,202 bp (19.82%) number of T's = 27,268,390 bp (29.53%) number of G's = 21,672,643 bp (23.47%) number of N's = 2,237 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 846,980 number of insertions = 7,179 mapped reads with insertion percentage = 0.48% number of deletions = 24,777 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.2795X There is a 2.32% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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 7584961 0.030431061594025074 0.33488965917948055 chr2 243199373 8286071 0.03407110346456362 0.34389813368558647 chr3 198022430 5800647 0.0292928785895618 0.2244567428410932 chr4 191154276 4611554 0.024124775529478608 0.21536983644990937 chr5 180915260 5288444 0.02923160821259633 0.22402466456349512 chr6 171115067 6183735 0.03613787557351685 0.2644222540558628 chr7 159138663 5255560 0.03302503553143462 0.39182386575851585 chr8 146364022 5102574 0.03486221497794041 0.27759705312450467 chr9 141213431 4052575 0.02869822630398379 0.29337035329709116 chr10 135534747 4471076 0.03298841145141917 0.2721546113190138 chr11 135006516 3765658 0.02789241668898411 0.2871925326030912 chr12 133851895 4025374 0.030073343377021295 0.24020216787405285 chr13 115169878 3588987 0.03116254929088316 0.23119037171657014 chr14 107349540 2741572 0.025538740082165234 0.24135663352214348 chr15 102531392 2550997 0.024880155728306118 0.23617334061950904 chr16 90354753 2830641 0.03132808077069283 0.24546151497353683 chr17 81195210 2458603 0.030280148299388597 0.2503239337419049 chr18 78077248 1932089 0.024745864505880125 0.41861856931195807 chr19 59128983 1892120 0.031999873902786385 0.28659921302990055 chr20 63025520 2666955 0.0423154779206899 0.2774100787936988 chr21 48129895 1362661 0.028312154015711025 0.23276508933451104 chr22 51304566 1046945 0.02040646830537461 0.19293375820665948 chrMT 16571 128290 7.741838150986664 6.246189401246872 chrX 155270560 4380443 0.02821167773208263 0.24545531446934135 chrY 59373566 388551 0.0065441748942618675 0.11404798768116227