BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524377.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 429,468 number of mapped reads = 398,995 (92.9%) number of supplementary alignments = 1,562 (0.36%) number of secondary alignments = 0 number of mapped bases = 23,430,402 bp number of sequenced bases = 23,423,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,236 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7651 >>>>>>> ACTG content number of A's = 5,832,245 bp (24.9%) number of C's = 4,602,621 bp (19.65%) number of T's = 7,261,272 bp (31%) number of G's = 5,724,476 bp (24.44%) number of N's = 3,126 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 113,911 number of insertions = 1,610 mapped reads with insertion percentage = 0.4% number of deletions = 4,254 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.38% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.1053X There is a 0.73% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 1972008 0.007911747589988954 0.1675954085060205 chr2 243199373 1900172 0.007813227380318945 0.11130754275124095 chr3 198022430 1605578 0.008108061293864538 0.09228723446976492 chr4 191154276 1530728 0.008007814588463613 0.09479555413628661 chr5 180915260 1492087 0.008247435843720424 0.09303337444420554 chr6 171115067 887751 0.005188035253494071 0.075415175052763 chr7 159138663 1303660 0.008191975321547097 0.1296146372791046 chr8 146364022 1237292 0.008453525552884847 0.10368646697347972 chr9 141213431 910292 0.006446214029032408 0.08981498414258894 chr10 135534747 1167250 0.008612182675192509 0.10701836902266287 chr11 135006516 946568 0.007011276403873721 0.09453121119585522 chr12 133851895 1085988 0.008113355436618959 0.09263361674504167 chr13 115169878 782099 0.006790829456292382 0.0843929409846768 chr14 107349540 666849 0.00621194091749252 0.0816862416991552 chr15 102531392 731458 0.007133990729395344 0.08631180681610184 chr16 90354753 697497 0.007719538561518728 0.09133588003437058 chr17 81195210 641203 0.00789705451836383 0.09375619356371101 chr18 78077248 659918 0.00845211655000955 0.12932922917259665 chr19 59128983 650262 0.010997347950327507 0.1419533857177411 chr20 63025520 639519 0.0101469849038929 0.1040624332801811 chr21 48129895 302968 0.0062947986900864835 0.08358760372333858 chr22 51304566 172179 0.0033560170843273483 0.05900698549556613 chrMT 16571 14698 0.8869712147727958 1.1134785471676958 chrX 155270560 1360619 0.008762891046441772 0.09817121319234311 chrY 59373566 71759 0.0012086018212212485 0.04225695289025422