BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008691.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 = 1,406,900 number of mapped reads = 1,054,179 (74.93%) number of supplementary alignments = 6,704 (0.48%) number of secondary alignments = 0 number of mapped bases = 69,245,551 bp number of sequenced bases = 69,212,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,710 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1135 >>>>>>> ACTG content number of A's = 20,702,346 bp (29.91%) number of C's = 12,306,193 bp (17.78%) number of T's = 21,177,408 bp (30.6%) number of G's = 15,014,243 bp (21.69%) number of N's = 12,725 bp (0.02%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 634,081 number of insertions = 6,088 mapped reads with insertion percentage = 0.57% number of deletions = 20,252 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2294X There is a 2.04% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 4583008 0.018387147769633842 0.30795326171025406 chr2 243199373 5613507 0.023081913948848874 0.2615598519362708 chr3 198022430 7284724 0.0367873679764459 0.2044332116194664 chr4 191154276 3352292 0.01753710181194168 0.14507152838849627 chr5 180915260 4144493 0.022908476598380922 0.16089154283808732 chr6 171115067 2563058 0.014978564102715747 0.13521685509395406 chr7 159138663 4506871 0.028320402566157036 0.33094969288025156 chr8 146364022 5072549 0.03465707576688484 0.388089125436808 chr9 141213431 2999930 0.021243942440574225 0.2303279897300401 chr10 135534747 3142310 0.02318453436888771 0.20008594500958488 chr11 135006516 2501018 0.018525165111289887 0.20983396158013687 chr12 133851895 2692217 0.020113402204727845 0.15383317873656036 chr13 115169878 1479707 0.012848038269173126 0.12090229086640292 chr14 107349540 3156134 0.029400535856977123 0.19516334883235603 chr15 102531392 2167502 0.021139886601754126 0.1552331476510655 chr16 90354753 1585408 0.01754648147840103 0.16080404812345386 chr17 81195210 1852038 0.02280969530099128 0.19016462856567815 chr18 78077248 1635958 0.020953069452447914 0.4159324528516338 chr19 59128983 996510 0.01685315642922524 0.2363889938084865 chr20 63025520 1293300 0.020520259095045942 0.15437204674047464 chr21 48129895 719565 0.014950479322674608 0.13723562385878446 chr22 51304566 785990 0.015320078918511853 0.13086964682875252 chrMT 16571 50209 3.0299318085812565 2.5466430454090814 chrX 155270560 4872096 0.03137810541805221 0.2074327717814813 chrY 59373566 195157 0.003286934121491035 0.076827067930732