BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716939.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 = 637,297 number of mapped reads = 493,807 (77.48%) number of supplementary alignments = 661 (0.1%) number of secondary alignments = 0 number of mapped bases = 26,249,366 bp number of sequenced bases = 26,242,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,772 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5033 >>>>>>> ACTG content number of A's = 5,304,675 bp (20.21%) number of C's = 4,445,781 bp (16.94%) number of T's = 8,910,508 bp (33.95%) number of G's = 7,581,321 bp (28.89%) number of N's = 509 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 172,055 number of insertions = 1,590 mapped reads with insertion percentage = 0.32% number of deletions = 3,716 mapped reads with deletion percentage = 0.75% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0085X std coverageData = 0.1066X There is a 0.77% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 2534970 0.01017036583431421 0.11990828428800542 chr2 243199373 2205680 0.009069431276864352 0.1319631594951933 chr3 198022430 1694438 0.008556798338450852 0.10044423627336961 chr4 191154276 1583768 0.008285286801536158 0.10235331751301355 chr5 180915260 2163353 0.01195782489547869 0.11883234886606604 chr6 171115067 1097145 0.006411738131744997 0.09103441661612689 chr7 159138663 1440073 0.009049171162132988 0.11037449077792753 chr8 146364022 1549006 0.01058324292290902 0.11347852668317933 chr9 141213431 1128851 0.00799393508114678 0.10275500852675919 chr10 135534747 1270569 0.009374489037855363 0.11563052344728338 chr11 135006516 1095354 0.008113341729372529 0.10346573253871195 chr12 133851895 1182211 0.008832232072620265 0.10219691889001206 chr13 115169878 421084 0.0036561990627445137 0.06620473096575892 chr14 107349540 1182069 0.011011402563997946 0.11594748087437967 chr15 102531392 503189 0.004907657939531339 0.07811482982071302 chr16 90354753 662340 0.0073304389421550405 0.09767387871927559 chr17 81195210 1007894 0.012413219942407933 0.12397815174224107 chr18 78077248 674654 0.008640852710382415 0.11181444379793463 chr19 59128983 668846 0.011311643902280545 0.12756704757019274 chr20 63025520 652621 0.010354868948324424 0.11376941973055633 chr21 48129895 342062 0.00710705892875935 0.0976897888456598 chr22 51304566 286184 0.005578138990591988 0.08301215680303539 chrMT 16571 15145 0.9139460503288879 1.1190596117204705 chrX 155270560 810821 0.005221987993087679 0.07893515943134427 chrY 59373566 77039 0.0012975302847735304 0.04686199706911309