BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174043.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,418,428 number of mapped reads = 3,325,415 (97.28%) number of supplementary alignments = 332,868 (9.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,665,211 number of mapped paired reads (second in pair) = 1,660,204 number of mapped paired reads (both in pair) = 3,264,242 number of mapped paired reads (singletons) = 61,173 number of mapped bases = 390,091,802 bp number of sequenced bases = 389,876,323 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,537,275 duplication rate = 64.53% >>>>>>> Insert size mean insert size = 807,810.3876 std insert size = 8,203,794.1027 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.6391 >>>>>>> ACTG content number of A's = 117,592,030 bp (30.16%) number of C's = 76,157,498 bp (19.53%) number of T's = 117,351,672 bp (30.1%) number of G's = 78,770,680 bp (20.2%) number of N's = 4,443 bp (0%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,934,103 number of insertions = 41,254 mapped reads with insertion percentage = 1.2% number of deletions = 85,792 mapped reads with deletion percentage = 2.51% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.126X std coverageData = 1.9122X There is a 2.77% of reference with a coverageData >= 1X There is a 2.16% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1.33% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.79% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 28353778 0.11375609772302232 1.4411357873064097 chr2 243199373 34636819 0.14242149793700332 5.426290806575639 chr3 198022430 38348557 0.19365764272259461 1.2559748691557142 chr4 191154276 18834938 0.09853265327949033 1.0220829571610264 chr5 180915260 27706375 0.15314559424119337 1.0998576887428264 chr6 171115067 16822709 0.09831226025233651 0.9684010258310887 chr7 159138663 22924307 0.1440524041602637 1.4209471504459457 chr8 146364022 19478241 0.1330807990504661 1.3975992926203598 chr9 141213431 15256881 0.1080412882256221 1.0755309259561705 chr10 135534747 21563676 0.15910072123423818 1.8006074679396937 chr11 135006516 13973620 0.10350330053699038 0.9234278545167788 chr12 133851895 17429119 0.1302119704767721 1.0162885171946552 chr13 115169878 9775893 0.08488237697013103 0.8233727082847729 chr14 107349540 12765490 0.11891518119220632 0.9804410439628358 chr15 102531392 9712697 0.0947290074828985 0.8553776226220091 chr16 90354753 13634576 0.15090048444933493 1.3462702087751681 chr17 81195210 16598195 0.20442332743520214 1.340129187822113 chr18 78077248 8133973 0.10417853098510849 1.4467878967638654 chr19 59128983 4998939 0.08454295586311708 1.0748293808522658 chr20 63025520 17016252 0.2699898707698088 1.549182912968725 chr21 48129895 5392982 0.11205056649302891 0.9728511047526052 chr22 51304566 2793030 0.05444018374504912 0.6234751662061078 chrMT 16571 1307771 78.91925653249653 58.47981318872991 chrX 155270560 11922194 0.07678335158963812 0.77272723870596 chrY 59373566 710790 0.01197148913036485 0.4854285929926042