BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094160.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 = 35,044 number of mapped reads = 900 (2.57%) number of supplementary alignments = 22 (0.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 305 number of mapped paired reads (second in pair) = 595 number of mapped paired reads (both in pair) = 484 number of mapped paired reads (singletons) = 416 number of mapped bases = 59,138 bp number of sequenced bases = 58,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 641 duplication rate = 24.56% >>>>>>> Insert size mean insert size = 7,488.8726 std insert size = 76,085.0117 median insert size = 31 >>>>>>> Mapping quality mean mapping quality = 3.7012 >>>>>>> ACTG content number of A's = 7,582 bp (12.86%) number of C's = 5,557 bp (9.42%) number of T's = 6,305 bp (10.69%) number of G's = 39,526 bp (67.03%) number of N's = 1 bp (0%) GC percentage = 76.45% >>>>>>> Mismatches and indels general error rate = 0.0296 number of mismatches = 1,288 number of insertions = 74 mapped reads with insertion percentage = 6% number of deletions = 40 mapped reads with deletion percentage = 3.78% homopolymer indels = 61.4% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0421X 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 577 2.314939066892034E-6 0.0019075907121451512 chr2 243199373 34635 1.4241401847693086E-4 0.1398804758010883 chr3 198022430 520 2.6259651495035183E-6 0.0018761120482955187 chr4 191154276 337 1.7629739028176382E-6 0.0013277691044532767 chr5 180915260 406 2.244144579069781E-6 0.003627027054615643 chr6 171115067 650 3.7986134791975973E-6 0.004212176697238262 chr7 159138663 532 3.3429965413244675E-6 0.0021002944584986344 chr8 146364022 559 3.819244595505855E-6 0.0022712016456825006 chr9 141213431 339 2.400621510286794E-6 0.0016851313114853506 chr10 135534747 464 3.4234763429336686E-6 0.0022693521449429926 chr11 135006516 156 1.1554997834326752E-6 0.002302921272814266 chr12 133851895 62 4.6319852251624827E-7 6.805867380160863E-4 chr13 115169878 333 2.8913810258616405E-6 0.002284375189830317 chr14 107349540 440 4.098759994686517E-6 0.003168902836495381 chr15 102531392 177 1.7263005655867814E-6 0.0015267581468443238 chr16 90354753 260 2.8775464639917723E-6 0.0016963308002032268 chr17 81195210 247 3.042051372242279E-6 0.0027921348708712912 chr18 78077248 63 8.068931937765019E-7 8.982719759070055E-4 chr19 59128983 36 6.088384777394192E-7 7.802807873164168E-4 chr20 63025520 78 1.2375939143381918E-6 0.001573272480226387 chr21 48129895 132 2.742578183476195E-6 0.0016560708504593342 chr22 51304566 30 5.847432760663057E-7 7.646848593646972E-4 chrMT 16571 1873 0.11302878522720415 0.596377797713899 chrX 155270560 15961 1.0279476032030798E-4 0.06776947520819539 chrY 59373566 271 4.564320761869011E-6 0.002572758519039023