BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094095.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 405,374 number of mapped reads = 386,534 (95.35%) number of supplementary alignments = 31,353 (7.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 194,303 number of mapped paired reads (second in pair) = 192,231 number of mapped paired reads (both in pair) = 383,184 number of mapped paired reads (singletons) = 3,350 number of mapped bases = 48,120,112 bp number of sequenced bases = 47,198,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 369,910 duplication rate = 53.3% >>>>>>> Insert size mean insert size = 2,119,120.7116 std insert size = 13,016,964.3593 median insert size = 146 >>>>>>> Mapping quality mean mapping quality = 41.7583 >>>>>>> ACTG content number of A's = 13,552,360 bp (28.71%) number of C's = 10,131,511 bp (21.47%) number of T's = 12,825,996 bp (27.17%) number of G's = 10,687,901 bp (22.64%) number of N's = 415 bp (0%) GC percentage = 44.11% >>>>>>> Mismatches and indels general error rate = 0.0356 number of mismatches = 1,620,322 number of insertions = 29,471 mapped reads with insertion percentage = 7.5% number of deletions = 127,507 mapped reads with deletion percentage = 31.73% homopolymer indels = 28.43% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 3.0061X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1303269 0.005228749259565536 1.9970106854239043 chr2 243199373 2072458 0.008521642035647847 2.457164750223887 chr3 198022430 801301 0.004046516346658305 1.3177091583333471 chr4 191154276 2214483 0.01158479447250241 3.3284574352462033 chr5 180915260 902833 0.004990363996934255 1.9153405732704238 chr6 171115067 1006419 0.005881533506339334 1.8070201967997461 chr7 159138663 1155048 0.007258123062149894 2.1097525117930385 chr8 146364022 899795 0.006147651504138087 1.548600912211783 chr9 141213431 982796 0.006959649610099764 2.907985872053677 chr10 135534747 905819 0.006683297235947915 2.2856869543046794 chr11 135006516 1522194 0.011274966906041779 2.66805252929531 chr12 133851895 1245406 0.009304358373110817 2.2044697721369766 chr13 115169878 679401 0.00589912060165593 1.4101691409135775 chr14 107349540 213790 0.0019915315892364326 0.7373388856276089 chr15 102531392 388819 0.003792194687067157 0.7472860450792748 chr16 90354753 252581 0.0027954367823904073 1.1643057739255316 chr17 81195210 330317 0.004068183332489687 0.9296419271568248 chr18 78077248 335231 0.004293581146712548 1.1354656070647695 chr19 59128983 88973 0.0015047273855530376 0.4445546067645445 chr20 63025520 226113 0.00358764195836861 1.1469998782148652 chr21 48129895 208281 0.004327476716913677 1.7489475301325026 chr22 51304566 51951 0.0010125999311640216 0.3341085372537302 chrMT 16571 350989 21.18091847202945 98.1277058678492 chrX 155270560 29150175 0.1877379395037926 10.066114755748574 chrY 59373566 831670 0.014007411985326939 2.79955784320327