BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472745.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,270,426 number of mapped reads = 18,062,968 (98.86%) number of supplementary alignments = 90,607 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,080,725 number of mapped paired reads (second in pair) = 8,982,243 number of mapped paired reads (both in pair) = 17,926,934 number of mapped paired reads (singletons) = 136,034 number of mapped bases = 1,783,450,217 bp number of sequenced bases = 1,783,206,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,199,446 duplication rate = 46.85% >>>>>>> Insert size mean insert size = 31,450.6265 std insert size = 1,717,706.9656 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 54.9232 >>>>>>> ACTG content number of A's = 494,250,390 bp (27.72%) number of C's = 400,834,447 bp (22.48%) number of T's = 491,326,534 bp (27.55%) number of G's = 396,454,648 bp (22.23%) number of N's = 340,691 bp (0.02%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 11,983,529 number of insertions = 98,690 mapped reads with insertion percentage = 0.54% number of deletions = 98,441 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.5761X std coverageData = 26.565X There is a 4.63% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 241197368 0.9676901386737167 56.580983805194 chr2 243199373 76030507 0.3126262459566456 11.410497187280216 chr3 198022430 199383480 1.0068732112821766 24.689712014240804 chr4 191154276 102811450 0.5378454102695563 28.418523664252103 chr5 180915260 106759258 0.5901064288330349 23.382932700366336 chr6 171115067 85131513 0.49751032736351614 16.2462383566469 chr7 159138663 45931058 0.2886228722431833 10.215165732018983 chr8 146364022 65920675 0.45038851829310894 18.774621741724758 chr9 141213431 130165349 0.9217632351132379 34.115610610765245 chr10 135534747 50365120 0.3716030104073607 15.044219762084879 chr11 135006516 50103844 0.3711216723791317 15.136092940175867 chr12 133851895 69017817 0.5156282397047871 18.442164566373048 chr13 115169878 29423104 0.2554756895722335 10.049882929001848 chr14 107349540 53521427 0.4985715541957609 23.5764797289282 chr15 102531392 59935213 0.5845547576297413 29.44501147764907 chr16 90354753 70824040 0.7838440994908148 28.892402360302874 chr17 81195210 64621274 0.7958754463471429 19.302052787390014 chr18 78077248 57386969 0.7350024555168748 42.27023768959071 chr19 59128983 40392283 0.6831215581705506 21.005260596267163 chr20 63025520 69788658 1.1073079285978125 39.183357588092086 chr21 48129895 6109108 0.126929593343181 7.410214836400458 chr22 51304566 15326241 0.2987305457373911 9.911130484688071 chrMT 16571 3444 0.20783296119727235 0.6325425111892204 chrX 155270560 90549623 0.5831731591616595 19.619426257817498 chrY 59373566 2751394 0.04634038656192555 2.144186693383903