BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094038.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 = 441,680 number of mapped reads = 420,893 (95.29%) number of supplementary alignments = 15,942 (3.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 211,539 number of mapped paired reads (second in pair) = 209,354 number of mapped paired reads (both in pair) = 417,738 number of mapped paired reads (singletons) = 3,155 number of mapped bases = 55,651,811 bp number of sequenced bases = 54,201,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 399,450 duplication rate = 50.79% >>>>>>> Insert size mean insert size = 550,381.1977 std insert size = 6,692,990.6872 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 41.1865 >>>>>>> ACTG content number of A's = 15,006,538 bp (27.69%) number of C's = 12,005,180 bp (22.15%) number of T's = 14,526,565 bp (26.8%) number of G's = 12,662,999 bp (23.36%) number of N's = 651 bp (0%) GC percentage = 45.51% >>>>>>> Mismatches and indels general error rate = 0.0454 number of mismatches = 2,392,937 number of insertions = 37,868 mapped reads with insertion percentage = 8.82% number of deletions = 198,389 mapped reads with deletion percentage = 43.8% homopolymer indels = 27.95% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 4.4618X 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% 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 1002202 0.0040208605939641776 1.5301333023436896 chr2 243199373 2808256 0.011547135033115403 3.499891248602701 chr3 198022430 1572903 0.007943054733749101 2.5989925600802066 chr4 191154276 851799 0.0044560813277334166 1.5676561935951885 chr5 180915260 324772 0.0017951608946641649 0.5899735617381041 chr6 171115067 1818992 0.010630226968850147 4.809803535879206 chr7 159138663 1352077 0.008496219425948049 2.8185787929258805 chr8 146364022 1337241 0.009136405120105268 3.5210909330198437 chr9 141213431 660720 0.004678875056863394 1.9694421439865553 chr10 135534747 901073 0.006648280385250581 2.0236004250807325 chr11 135006516 1984108 0.014696386950686143 3.973816471051219 chr12 133851895 1868943 0.013962768326888461 3.887891323603979 chr13 115169878 976773 0.008481149906228086 2.1962119777092415 chr14 107349540 316278 0.0029462445763624137 1.2117767559034491 chr15 102531392 398252 0.0038841957787913383 0.9718871312018392 chr16 90354753 516280 0.005713921878575663 2.1080500175369705 chr17 81195210 1609666 0.0198246423649868 4.838727390742617 chr18 78077248 154519 0.0019790528477643065 0.6049556807387325 chr19 59128983 268511 0.004541106347119145 1.2199201401024444 chr20 63025520 287711 0.004564992085745584 1.6827129449145597 chr21 48129895 359220 0.0074635525383963544 2.6917966235392727 chr22 51304566 123636 0.0024098439893244588 0.5300543649393851 chrMT 16571 3555860 214.5833081890049 880.046166886446 chrX 155270560 30101287 0.19386345357419976 13.013925342071554 chrY 59373566 500732 0.008433584737019164 1.9806648507896931