BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240062.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 = 2,445,223 number of mapped reads = 2,088,971 (85.43%) number of supplementary alignments = 19,944 (0.82%) number of secondary alignments = 0 number of mapped bases = 138,356,690 bp number of sequenced bases = 138,264,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,706 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5935 >>>>>>> ACTG content number of A's = 39,693,381 bp (28.71%) number of C's = 25,857,830 bp (18.7%) number of T's = 43,736,652 bp (31.63%) number of G's = 28,964,730 bp (20.95%) number of N's = 12,249 bp (0.01%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,286,697 number of insertions = 10,708 mapped reads with insertion percentage = 0.51% number of deletions = 53,041 mapped reads with deletion percentage = 2.5% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.6675X There is a 2.96% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15098997 0.06057757023602361 1.4594866876555908 chr2 243199373 10554020 0.0433965756975862 0.48801649859900065 chr3 198022430 20183074 0.10192317102663571 0.4468794128629572 chr4 191154276 6889971 0.036044032831366014 0.27529238975809356 chr5 180915260 6031819 0.03334057613492637 0.27111171771543885 chr6 171115067 4832513 0.028241306184919414 0.2434043185317266 chr7 159138663 4167741 0.026189367947624394 0.37112678517064773 chr8 146364022 10557048 0.07212870933541304 1.6942923462104698 chr9 141213431 2464371 0.017451392424563356 0.3818773215832377 chr10 135534747 4174626 0.03080114946464614 0.44842267278484615 chr11 135006516 2149348 0.015920327875137523 0.2383943604897015 chr12 133851895 12498623 0.09337651140463869 0.4737443240109619 chr13 115169878 6320673 0.0548813032518798 0.3269789106513254 chr14 107349540 1692434 0.015765638120107454 0.20663062140116253 chr15 102531392 4526802 0.044150400298866514 0.2925426932453576 chr16 90354753 2307025 0.025532967811886995 0.28741476322313414 chr17 81195210 3200198 0.039413630434603227 0.30726152675869756 chr18 78077248 5820418 0.07454691538308317 0.962141445055594 chr19 59128983 3239626 0.054789137841251216 0.823854945109538 chr20 63025520 3812988 0.06049911210569941 0.36471096317413365 chr21 48129895 1894251 0.039357056565363376 0.2951746504862512 chr22 51304566 1888037 0.03680056469047999 0.26312524469186205 chrMT 16571 26451 1.5962223160943818 5.359259750705772 chrX 155270560 3636598 0.023421040022010613 0.2519995920003792 chrY 59373566 389038 0.006552377197623602 0.2549135036688543