BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714197.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 = 93,824 number of mapped reads = 23,827 (25.4%) number of supplementary alignments = 953 (1.02%) number of secondary alignments = 0 number of mapped bases = 2,687,313 bp number of sequenced bases = 2,640,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,290 duplication rate = 50% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.0105 >>>>>>> ACTG content number of A's = 559,473 bp (21.19%) number of C's = 482,269 bp (18.27%) number of T's = 524,493 bp (19.87%) number of G's = 1,073,781 bp (40.67%) number of N's = 36 bp (0%) GC percentage = 58.94% >>>>>>> Mismatches and indels general error rate = 0.0359 number of mismatches = 87,786 number of insertions = 1,493 mapped reads with insertion percentage = 5.02% number of deletions = 5,731 mapped reads with deletion percentage = 23.01% homopolymer indels = 32.81% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 0.7665X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 60478 2.4263931522962987E-4 0.20787144788527762 chr2 243199373 705556 0.0029011423479286683 2.569352052705273 chr3 198022430 38789 1.9588185035402303E-4 0.05524422471123107 chr4 191154276 40879 2.1385344265068912E-4 0.06377295588322697 chr5 180915260 56436 3.119471513901039E-4 0.09533784253508763 chr6 171115067 44242 2.585511654564002E-4 0.07568419243322108 chr7 159138663 70137 4.407288504114176E-4 0.308281910489035 chr8 146364022 130274 8.900684623165111E-4 0.5159095125726157 chr9 141213431 14447 1.0230613262275314E-4 0.02796510469399752 chr10 135534747 60397 4.456200445779413E-4 0.3069446193165717 chr11 135006516 21479 1.5909602466891303E-4 0.040951252872265455 chr12 133851895 50237 3.753178092846575E-4 0.1020843518687185 chr13 115169878 15879 1.3787459252149247E-4 0.047247875930892594 chr14 107349540 49799 4.6389579312589507E-4 0.1635237663500021 chr15 102531392 46859 4.5702100679565535E-4 0.12686141778475116 chr16 90354753 14342 1.5872988994834617E-4 0.05780593277950628 chr17 81195210 60939 7.505245691217499E-4 0.16766029877078187 chr18 78077248 23758 3.0428838885304975E-4 0.06814484650974939 chr19 59128983 20280 3.429790091265395E-4 0.11716124727570415 chr20 63025520 60089 9.534074451111233E-4 0.3643993338169112 chr21 48129895 8723 1.8123870829138522E-4 0.043078749443424 chr22 51304566 5899 1.1498001951717125E-4 0.04290338143228614 chrMT 16571 1555 0.0938386337577696 0.47198098890934276 chrX 155270560 1081020 0.006962169776421235 0.8522172008875686 chrY 59373566 4820 8.118090801553001E-5 0.02817083481064252