BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240252.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 = 1,190,973 number of mapped reads = 901,376 (75.68%) number of supplementary alignments = 7,859 (0.66%) number of secondary alignments = 0 number of mapped bases = 59,649,035 bp number of sequenced bases = 59,621,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,365 duplication rate = 6.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0756 >>>>>>> ACTG content number of A's = 17,393,543 bp (29.17%) number of C's = 11,208,025 bp (18.8%) number of T's = 18,636,776 bp (31.26%) number of G's = 12,348,680 bp (20.71%) number of N's = 34,185 bp (0.06%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 528,656 number of insertions = 4,210 mapped reads with insertion percentage = 0.46% number of deletions = 15,682 mapped reads with deletion percentage = 1.72% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.2522X There is a 1.18% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 4618581 0.01852986757453254 0.3531611795194705 chr2 243199373 6312944 0.02595789587006871 0.2863591100416745 chr3 198022430 3767696 0.019026612288315016 0.20741390527480166 chr4 191154276 3962562 0.020729653989011474 0.22325697519225146 chr5 180915260 3328264 0.018396811855451 0.2107887217255658 chr6 171115067 3303033 0.01930299334774535 0.22789575860028705 chr7 159138663 3522318 0.0221336407733927 0.30627097913677165 chr8 146364022 3273121 0.02236287958799055 0.3278850757520574 chr9 141213431 2177931 0.015422973470561735 0.225638233879456 chr10 135534747 2804040 0.020688716820344233 0.2551838740420695 chr11 135006516 2566202 0.019007986251567296 0.24539552103779239 chr12 133851895 2839374 0.02121280389792016 0.22102377921347047 chr13 115169878 1570009 0.013632114813909935 0.17732759389821018 chr14 107349540 1988703 0.018525491585711498 0.21414707516007764 chr15 102531392 1681689 0.01640169871096649 0.21778912080243945 chr16 90354753 1728197 0.019126796793966113 0.21697447552743496 chr17 81195210 1407843 0.017338990809925858 0.20218230652083805 chr18 78077248 1563832 0.020029292016030074 0.3490381086279845 chr19 59128983 1074382 0.018170141705295354 0.27582037818631155 chr20 63025520 1269915 0.020149218919574167 0.2202137013717325 chr21 48129895 970551 0.020165242413265186 0.2160246551510558 chr22 51304566 531384 0.010357440700307259 0.14565958590892367 chrMT 16571 10199 0.615472813952085 1.227975180736819 chrX 155270560 3212640 0.02069059324575116 0.22254065511521567 chrY 59373566 163625 0.002755856031958734 0.07590255562453396