BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094098.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 = 524 number of mapped reads = 309 (58.97%) number of supplementary alignments = 22 (4.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 163 number of mapped paired reads (second in pair) = 146 number of mapped paired reads (both in pair) = 266 number of mapped paired reads (singletons) = 43 number of mapped bases = 35,159 bp number of sequenced bases = 34,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109 duplication rate = 11.26% >>>>>>> Insert size mean insert size = 787,279.4476 std insert size = 5,688,706.9917 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 6.7292 >>>>>>> ACTG content number of A's = 11,276 bp (32.53%) number of C's = 7,230 bp (20.86%) number of T's = 9,055 bp (26.12%) number of G's = 7,100 bp (20.48%) number of N's = 0 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0374 number of mismatches = 1,233 number of insertions = 21 mapped reads with insertion percentage = 6.8% number of deletions = 114 mapped reads with deletion percentage = 35.28% homopolymer indels = 28.89% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.011X There is a 0% 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 1771 7.1052982451746835E-6 0.010462124499867357 chr2 243199373 877 3.606094823279006E-6 0.002596018794506849 chr3 198022430 245 1.2372335800545424E-6 0.001236983493073715 chr4 191154276 927 4.849486076890061E-6 0.0026417108704052984 chr5 180915260 7183 3.970367121048827E-5 0.03580652248073705 chr6 171115067 117 6.837504262555675E-7 8.268917454787671E-4 chr7 159138663 545 3.4246863064320204E-6 0.0022574704535426276 chr8 146364022 249 1.7012377536331982E-6 0.001609170990598204 chr9 141213431 66 4.6737763917088027E-7 6.836500718415985E-4 chr10 135534747 729 5.378694512928113E-6 0.002643314057998101 chr11 135006516 1452 1.0755036445796438E-5 0.004541047406951439 chr12 133851895 2599 1.9416983226124665E-5 0.012934602588694284 chr13 115169878 103 8.943310680593063E-7 9.456903659397439E-4 chr14 107349540 109 1.0153746350473416E-6 9.936939015312174E-4 chr15 102531392 454 4.427912185177394E-6 0.0025332848173392573 chr16 90354753 66 7.304541023979115E-7 8.546657643984084E-4 chr17 81195210 33 4.0642791612953524E-7 6.375168632639331E-4 chr18 78077248 34 4.354661680698582E-7 6.598984607036712E-4 chr19 59128983 46 7.779602771114801E-7 8.820202219276422E-4 chr20 63025520 32 5.077308366515659E-7 7.125521586950414E-4 chr21 48129895 193 4.009981737961406E-6 0.0020024898646454786 chr22 51304566 30 5.847432760663057E-7 7.646848593646972E-4 chrMT 16571 6278 0.3788546255506608 1.9422651449714214 chrX 155270560 10605 6.830013365057741E-5 0.010201559245688904 chrY 59373566 416 7.006485007149478E-6 0.00307659610896339