BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 409,716 number of mapped reads = 174,190 (42.51%) number of supplementary alignments = 5,715 (1.39%) number of secondary alignments = 0 number of mapped bases = 22,041,665 bp number of sequenced bases = 21,581,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,641 duplication rate = 41.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9321 >>>>>>> ACTG content number of A's = 5,553,917 bp (25.73%) number of C's = 4,235,521 bp (19.63%) number of T's = 5,286,553 bp (24.5%) number of G's = 6,505,164 bp (30.14%) number of N's = 291 bp (0%) GC percentage = 49.77% >>>>>>> Mismatches and indels general error rate = 0.0444 number of mismatches = 879,916 number of insertions = 25,352 mapped reads with insertion percentage = 13.77% number of deletions = 76,592 mapped reads with deletion percentage = 41.07% homopolymer indels = 32.37% >>>>>>> Coverage mean coverageData = 0.0071X std coverageData = 3.1076X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 1559195 0.0062555310544241335 1.127467502227328 chr2 243199373 3491792 0.014357734384455012 9.395550909208444 chr3 198022430 1893405 0.009561568353645595 3.804375663931218 chr4 191154276 617032 0.0032279267454106025 0.8492936139562637 chr5 180915260 1121158 0.0061971444531544765 1.123668220791257 chr6 171115067 697865 0.0040783375317849715 0.8290029976778699 chr7 159138663 551401 0.003464909090005362 0.617324040775906 chr8 146364022 867796 0.005929025372095883 1.7007829472125393 chr9 141213431 507052 0.0035906782832859576 0.6564424414010893 chr10 135534747 1437483 0.010606010870408014 3.634818258208086 chr11 135006516 964972 0.007147595750119202 1.3368728438721666 chr12 133851895 753808 0.005631657288079486 1.065440667359063 chr13 115169878 671228 0.005828155865546719 1.3020752945256984 chr14 107349540 717103 0.006680075201067466 1.728034491905488 chr15 102531392 739748 0.007214844015772263 1.3687181965677957 chr16 90354753 609990 0.006751056029116697 0.9423694755022094 chr17 81195210 848107 0.010445283656511265 2.154516267400978 chr18 78077248 681071 0.008723040545691365 1.3736842034247443 chr19 59128983 351282 0.00594094439270163 1.0391704711515302 chr20 63025520 433088 0.006871629143242293 1.2895466436081615 chr21 48129895 101136 0.002101313539121579 0.30650286456694 chr22 51304566 253037 0.004932056144866326 1.1330942638017472 chrMT 16571 116559 7.033914670206988 58.28492257656291 chrX 155270560 2010637 0.012949248073813865 1.6463496876118067 chrY 59373566 45720 7.700396503049859E-4 0.19402589678740872