BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525233.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 = 402,525 number of mapped reads = 365,110 (90.7%) number of supplementary alignments = 1,434 (0.36%) number of secondary alignments = 0 number of mapped bases = 22,989,242 bp number of sequenced bases = 22,980,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,222 duplication rate = 1.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8694 >>>>>>> ACTG content number of A's = 6,065,512 bp (26.39%) number of C's = 4,853,440 bp (21.12%) number of T's = 7,032,634 bp (30.6%) number of G's = 5,028,355 bp (21.88%) number of N's = 558 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 113,272 number of insertions = 2,029 mapped reads with insertion percentage = 0.55% number of deletions = 5,190 mapped reads with deletion percentage = 1.41% homopolymer indels = 40.07% >>>>>>> Coverage mean coverageData = 0.0074X std coverageData = 0.1058X There is a 0.71% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1869104 0.007498894054911903 0.16853287822024163 chr2 243199373 1947182 0.008006525576034276 0.105919804587077 chr3 198022430 1511627 0.007633615040477991 0.0895739108351506 chr4 191154276 1459689 0.007636182828575595 0.0922370068913073 chr5 180915260 1388599 0.00767541112894512 0.0901670908898604 chr6 171115067 1320994 0.00771991632975254 0.09326183214822192 chr7 159138663 1287448 0.008090101900629892 0.13475727112111507 chr8 146364022 1171861 0.008006482631366881 0.1016686283831842 chr9 141213431 960391 0.006800989064560013 0.09347053933024432 chr10 135534747 1104753 0.008151068448890084 0.11129164827038077 chr11 135006516 1053420 0.007802734499125954 0.0960731340007936 chr12 133851895 1038847 0.007761167669684467 0.09066072515866579 chr13 115169878 722603 0.006274236046338436 0.08093361477118069 chr14 107349540 687754 0.006406678594058251 0.08367764468047964 chr15 102531392 654180 0.006380289853082264 0.08173329350854326 chr16 90354753 685484 0.007586584847395908 0.09228296318396759 chr17 81195210 623006 0.0076729403126120374 0.09148430611680056 chr18 78077248 632060 0.008095316064418663 0.14958966668867837 chr19 59128983 463553 0.007839691746431695 0.12364985221414693 chr20 63025520 485771 0.007707528632845869 0.09054298614212798 chr21 48129895 307568 0.006390373384359139 0.08474996403894854 chr22 51304566 277056 0.005400221103127547 0.0752801706538408 chrMT 16571 4718 0.28471425985154786 0.5550856039410508 chrX 155270560 1256194 0.008090355312687737 0.09426373901252644 chrY 59373566 75380 0.0012695885573051145 0.055441101404630516