BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237297.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 = 2,155,294 number of mapped reads = 1,978,526 (91.8%) number of supplementary alignments = 17,109 (0.79%) number of secondary alignments = 0 number of mapped bases = 136,208,081 bp number of sequenced bases = 136,147,034 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,445 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1449 >>>>>>> ACTG content number of A's = 39,540,858 bp (29.04%) number of C's = 25,178,673 bp (18.49%) number of T's = 43,050,593 bp (31.62%) number of G's = 28,374,671 bp (20.84%) number of N's = 2,239 bp (0%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,014,861 number of insertions = 10,264 mapped reads with insertion percentage = 0.51% number of deletions = 34,958 mapped reads with deletion percentage = 1.75% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.5494X There is a 2.29% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 11543684 0.046313561642039 0.5050327319985469 chr2 243199373 7460766 0.03067757086692818 0.38933898970555947 chr3 198022430 9331813 0.0471250302301613 0.3623111151670915 chr4 191154276 8383821 0.0438589247148204 0.3621373102138757 chr5 180915260 5652330 0.031242969774910086 0.2914154263178494 chr6 171115067 22041608 0.12881161423383014 0.6693845421766174 chr7 159138663 6042815 0.03797201061064589 0.4259453949689137 chr8 146364022 4248481 0.029026812340535436 1.746061442515286 chr9 141213431 5936852 0.04204169502828665 0.3927678644512674 chr10 135534747 6783003 0.05004622910462953 0.426573740590203 chr11 135006516 6183446 0.04580109303761309 0.4227295417080677 chr12 133851895 4061787 0.030345382857672652 0.29143894094273953 chr13 115169878 11341907 0.09847980389455653 0.5465112756372095 chr14 107349540 2490875 0.02320340636764722 0.27279077737747953 chr15 102531392 2972714 0.028993208245919454 0.2835663627929037 chr16 90354753 3118348 0.03451227408036852 0.3161994991288018 chr17 81195210 4630580 0.05703021151124555 0.41329331710954714 chr18 78077248 2362333 0.03025635585926389 0.5056185102765481 chr19 59128983 1873974 0.03169298548564585 0.39820633278172873 chr20 63025520 2151790 0.03414156678120228 0.3082228566099609 chr21 48129895 2184213 0.045381628195947654 0.36506091514643174 chr22 51304566 848252 0.016533655113659864 0.20054830852652314 chrMT 16571 20107 1.2133848289179892 1.8669786579413374 chrX 155270560 4253926 0.027396861323872344 0.2921285083887403 chrY 59373566 288656 0.00486169215438399 0.14006100624058546