BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238490.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 = 3,312,476 number of mapped reads = 3,056,271 (92.27%) number of supplementary alignments = 22,105 (0.67%) number of secondary alignments = 0 number of mapped bases = 187,400,882 bp number of sequenced bases = 187,322,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,092,406 duplication rate = 22.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.175 >>>>>>> ACTG content number of A's = 45,207,142 bp (24.13%) number of C's = 32,237,598 bp (17.21%) number of T's = 63,768,050 bp (34.04%) number of G's = 46,097,004 bp (24.61%) number of N's = 12,419 bp (0.01%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 972,842 number of insertions = 11,061 mapped reads with insertion percentage = 0.36% number of deletions = 46,813 mapped reads with deletion percentage = 1.52% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 0.9105X There is a 2.31% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 16409831 0.06583667047312994 0.903706837275758 chr2 243199373 31355515 0.1289292592049569 1.89723488291269 chr3 198022430 12121155 0.06121102038794292 0.5534412702028471 chr4 191154276 2412255 0.01261941427875775 0.21835352262399907 chr5 180915260 1954055 0.010800940727719708 0.21036467321870428 chr6 171115067 21726523 0.12697025095984096 1.239673387375466 chr7 159138663 27005181 0.16969591481361132 1.8943084692280885 chr8 146364022 20957884 0.14319013452636606 0.968762005793427 chr9 141213431 3513889 0.024883532501947355 0.3762413481296985 chr10 135534747 12285576 0.09064521292093458 0.6861161951721148 chr11 135006516 8417369 0.06234787215751868 0.5853953995162522 chr12 133851895 1205239 0.009004272969015494 0.17556366701519083 chr13 115169878 3620742 0.031438272427448434 0.5291722229356489 chr14 107349540 642517 0.005985279489786356 0.15778126978735021 chr15 102531392 855578 0.0083445468096249 0.38914963545486286 chr16 90354753 812663 0.008994136700257484 0.22800204526113857 chr17 81195210 1475774 0.018175628833277235 0.2801324173844603 chr18 78077248 9714428 0.1244207275338393 1.474864889957957 chr19 59128983 2446231 0.041371098839971594 0.6087486051042793 chr20 63025520 3483104 0.055264978377013 0.5221127300852367 chr21 48129895 2794958 0.058071142685850445 0.5278552712520446 chr22 51304566 287390 0.005601645670289853 0.12514274846012644 chrMT 16571 36047 2.1753062579204636 3.4622300571599025 chrX 155270560 1662250 0.010705506568663113 0.21183553429273827 chrY 59373566 204728 0.0034481338041915826 0.2406484871730124