BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234114.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,305,794 number of mapped reads = 846,476 (64.82%) number of supplementary alignments = 3,368 (0.26%) number of secondary alignments = 0 number of mapped bases = 51,412,059 bp number of sequenced bases = 51,376,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,212 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5272 >>>>>>> ACTG content number of A's = 13,168,945 bp (25.63%) number of C's = 8,938,035 bp (17.4%) number of T's = 16,402,457 bp (31.93%) number of G's = 12,861,866 bp (25.03%) number of N's = 5,402 bp (0.01%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 473,114 number of insertions = 4,279 mapped reads with insertion percentage = 0.5% number of deletions = 19,855 mapped reads with deletion percentage = 2.31% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.1827X There is a 1.44% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 4456497 0.01787958233411984 0.2403733366737597 chr2 243199373 3602311 0.014812172233684171 0.20607333844424225 chr3 198022430 4130556 0.02085903096937049 0.1648392848728117 chr4 191154276 2585262 0.013524479044350543 0.1387276834795651 chr5 180915260 3004098 0.016605000595306334 0.14811077027137418 chr6 171115067 3296716 0.019266076668748286 0.1818683248284665 chr7 159138663 3115021 0.019574256445776473 0.2622479546334424 chr8 146364022 2455636 0.01677759306177033 0.20012557191828909 chr9 141213431 2079884 0.014728655661655866 0.17432627965655548 chr10 135534747 2542473 0.018758827948378434 0.17544262952934697 chr11 135006516 2451361 0.0181573532347135 0.19689149210255863 chr12 133851895 2061073 0.015398160780615022 0.14114064803442444 chr13 115169878 1804572 0.015668784506309888 0.15144186718185004 chr14 107349540 2075038 0.019329733504214363 0.16492187915938866 chr15 102531392 1254584 0.012236096433763428 0.13190195262991136 chr16 90354753 1467970 0.01624673801056155 0.15500369134256217 chr17 81195210 1441977 0.017759385067173297 0.16377457114582025 chr18 78077248 1194925 0.015304394437672803 0.25414094345250443 chr19 59128983 1372819 0.023217361949215327 0.2117627226872655 chr20 63025520 1229503 0.01950801833923782 0.16663118733513638 chr21 48129895 776171 0.01612658826702198 0.14760811799175264 chr22 51304566 545572 0.010633985287001551 0.11664813729265369 chrMT 16571 33396 2.0153279826202404 2.4109964201727934 chrX 155270560 2222777 0.014315508361662378 0.14663671463243502 chrY 59373566 211867 0.0035683724976195634 0.07682677322439689