BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237857.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 = 3,083,478 number of mapped reads = 2,714,069 (88.02%) number of supplementary alignments = 19,935 (0.65%) number of secondary alignments = 0 number of mapped bases = 197,927,083 bp number of sequenced bases = 197,837,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,240 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5044 >>>>>>> ACTG content number of A's = 59,733,144 bp (30.19%) number of C's = 39,658,519 bp (20.05%) number of T's = 58,406,985 bp (29.52%) number of G's = 39,696,003 bp (20.06%) number of N's = 343,135 bp (0.17%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,723,821 number of insertions = 15,553 mapped reads with insertion percentage = 0.57% number of deletions = 49,006 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.7337X There is a 3.46% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 15319366 0.0614616964184013 1.5751428410640027 chr2 243199373 19139095 0.07869713956869454 0.7579470459243345 chr3 198022430 16098104 0.08129434630208306 0.4842641461389767 chr4 191154276 15126770 0.07913383010066696 0.5112868385703789 chr5 180915260 13040321 0.07207971842729022 0.44692737233412666 chr6 171115067 9699050 0.05668144933140224 0.42763176365021976 chr7 159138663 9430305 0.05925841541096773 0.759668696531417 chr8 146364022 7643101 0.05221980713265723 0.6290930145475141 chr9 141213431 6899990 0.04886213691670731 0.6489333119664031 chr10 135534747 9120822 0.06729508264032101 0.7976590235117359 chr11 135006516 10518325 0.07790975807419546 0.684785743293169 chr12 133851895 8960482 0.0669432584424748 0.4353384417811516 chr13 115169878 5196232 0.04511797781013539 0.34698154096398054 chr14 107349540 5618197 0.05233554796788137 0.4283245139662873 chr15 102531392 4717695 0.04601220082918605 0.35350282356637774 chr16 90354753 8821466 0.09763145498278325 0.6081053399696326 chr17 81195210 5028120 0.06192631314088602 0.4839221304885529 chr18 78077248 4956692 0.06348446092772123 1.3192573836544188 chr19 59128983 2916184 0.04931902853800141 0.975752280945196 chr20 63025520 3001357 0.04762129689687606 0.3932482972611716 chr21 48129895 2351060 0.04884822624275412 0.41572565434693015 chr22 51304566 1599836 0.031183111460293806 0.2844984846573948 chrMT 16571 77922 4.70231126667069 3.6082389324529034 chrX 155270560 12022821 0.07743142679462224 0.5063172698949457 chrY 59373566 623770 0.010505853732955841 0.31780998963621465