BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,709,622 number of mapped reads = 1,559,676 (91.23%) number of supplementary alignments = 49,957 (2.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 782,712 number of mapped paired reads (second in pair) = 776,964 number of mapped paired reads (both in pair) = 1,549,034 number of mapped paired reads (singletons) = 10,642 number of mapped bases = 191,664,097 bp number of sequenced bases = 191,481,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,139 duplication rate = 14.76% >>>>>>> Insert size mean insert size = 106,389.7832 std insert size = 3,182,336.7402 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.1126 >>>>>>> ACTG content number of A's = 56,754,287 bp (29.64%) number of C's = 38,688,796 bp (20.21%) number of T's = 56,652,770 bp (29.59%) number of G's = 39,379,353 bp (20.57%) number of N's = 5,889 bp (0%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,466,554 number of insertions = 33,030 mapped reads with insertion percentage = 1.98% number of deletions = 87,446 mapped reads with deletion percentage = 5.37% homopolymer indels = 43.86% >>>>>>> Coverage mean coverageData = 0.0619X std coverageData = 0.7179X There is a 3.85% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 15687508 0.06293869173549622 1.4103827902518307 chr2 243199373 17376239 0.071448535354571 1.0716918891812788 chr3 198022430 12969019 0.06549267676394033 0.36848824259404367 chr4 191154276 12169333 0.06366236348278183 0.4285521025109943 chr5 180915260 11269978 0.062294236539250473 0.3662904569840942 chr6 171115067 11094233 0.06483492771562892 0.4383819446117203 chr7 159138663 10360208 0.06510176599887608 0.8958138330125671 chr8 146364022 9321286 0.06368563717113486 0.531801137221725 chr9 141213431 8574728 0.060721759532915816 1.0254899053795368 chr10 135534747 11298566 0.08336287372860925 0.8392288969383466 chr11 135006516 8741414 0.06474808964035485 0.5000681619340513 chr12 133851895 8629214 0.06446837379478267 0.37101539782465265 chr13 115169878 5708289 0.04956407959379795 0.32097021857782726 chr14 107349540 5729379 0.05337124872635691 0.35647158401400647 chr15 102531392 5684294 0.05543954772407655 0.34114553284639026 chr16 90354753 5272013 0.05834793217795637 0.619860545749969 chr17 81195210 5485473 0.06755907152651 0.47293092850059276 chr18 78077248 5066572 0.06489178512029523 0.8577539912485412 chr19 59128983 3691178 0.062425866516256506 0.7131764064415684 chr20 63025520 3833788 0.06082913714952292 0.36863871379420515 chr21 48129895 2361407 0.049063206973545236 0.338295653314805 chr22 51304566 2212937 0.043133334370278074 0.31273130801635624 chrMT 16571 204206 12.323094562790416 7.353997684378716 chrX 155270560 8469690 0.05454794521253739 0.35208398804020574 chrY 59373566 453145 0.007632100116742188 0.5229432665781841