BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524709.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,142,632 number of mapped reads = 1,056,256 (92.44%) number of supplementary alignments = 3,962 (0.35%) number of secondary alignments = 0 number of mapped bases = 62,363,197 bp number of sequenced bases = 62,343,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,338 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8542 >>>>>>> ACTG content number of A's = 15,809,132 bp (25.36%) number of C's = 11,636,396 bp (18.66%) number of T's = 20,030,699 bp (32.13%) number of G's = 14,858,329 bp (23.83%) number of N's = 8,885 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 315,182 number of insertions = 4,725 mapped reads with insertion percentage = 0.44% number of deletions = 12,231 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2136X There is a 1.86% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 4994485 0.02003800423831241 0.365599977838188 chr2 243199373 5252336 0.02159683199512196 0.28994350291950016 chr3 198022430 4063772 0.02052177624524656 0.1530738957293053 chr4 191154276 4046404 0.021168263063076863 0.16997316613212196 chr5 180915260 3701617 0.02046050178409494 0.15288316987294318 chr6 171115067 3575433 0.020894904596566004 0.16878125944280506 chr7 159138663 3461672 0.02175255173533788 0.2391995508366971 chr8 146364022 3198117 0.02185043124873953 0.23532770523247631 chr9 141213431 2623552 0.018578629393970324 0.18032401043469484 chr10 135534747 3028264 0.022343082250339832 0.22301488946560524 chr11 135006516 2814755 0.020849030723820768 0.18118345186995913 chr12 133851895 2858661 0.02135689599314227 0.1563272243205636 chr13 115169878 1975585 0.017153660612543153 0.13965843432193686 chr14 107349540 1870435 0.01742378216059426 0.1463829813132049 chr15 102531392 1768793 0.01725123365144599 0.1401706764207998 chr16 90354753 1824101 0.02018821300966868 0.16011027558041213 chr17 81195210 1653758 0.020367679324925694 0.15691812481789866 chr18 78077248 1659558 0.021255334204402287 0.29645613496248363 chr19 59128983 1287356 0.021771996315241883 0.2876866978474187 chr20 63025520 1349542 0.021412627773638362 0.1578934990341517 chr21 48129895 834613 0.017340843980648616 0.15306090201758377 chr22 51304566 744556 0.014512470488494142 0.12801460570838985 chrMT 16571 32819 1.9805081165892222 1.8986980294967464 chrX 155270560 3534229 0.022761745690876623 0.171976034388844 chrY 59373566 208784 0.00351644703301129 0.13427228028658503