BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251079.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 4,265,113 number of mapped reads = 4,029,842 (94.48%) number of supplementary alignments = 33,765 (0.79%) number of secondary alignments = 0 number of mapped bases = 311,736,615 bp number of sequenced bases = 311,530,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 818,083 duplication rate = 17.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8003 >>>>>>> ACTG content number of A's = 91,361,637 bp (29.33%) number of C's = 61,900,711 bp (19.87%) number of T's = 92,437,289 bp (29.67%) number of G's = 65,828,233 bp (21.13%) number of N's = 2,556 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,913,463 number of insertions = 39,042 mapped reads with insertion percentage = 0.95% number of deletions = 115,689 mapped reads with deletion percentage = 2.82% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.1007X std coverageData = 1.1756X There is a 6.82% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% 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 25239517 0.10126160126999242 2.5332187853704506 chr2 243199373 26715109 0.10984859323629917 1.4190301415761466 chr3 198022430 20600984 0.10403358851822998 0.4463231218829462 chr4 191154276 20266016 0.10601916119312968 0.5348919545455276 chr5 180915260 18922291 0.10459201175180026 0.4635681234481006 chr6 171115067 17894241 0.10457431548093891 0.6394479401779818 chr7 159138663 17221432 0.10821651806889945 1.8029478355612503 chr8 146364022 15636459 0.10683266820858475 0.751905397890174 chr9 141213431 12997255 0.09203979329699878 1.5639271692903436 chr10 135534747 17928785 0.1322818347091466 1.0873121588541088 chr11 135006516 14114083 0.1045437169862231 0.6745780102695166 chr12 133851895 13736912 0.10262769906993098 0.462728103330875 chr13 115169878 9623233 0.08355685676770448 0.38962111290700757 chr14 107349540 9451856 0.08804747556440391 0.6773312304877184 chr15 102531392 8673061 0.08458932265349524 0.3962495331915651 chr16 90354753 8665075 0.0959005997172058 0.8382593179726732 chr17 81195210 8012824 0.09868592001917355 0.5761285807085433 chr18 78077248 8128699 0.10411098249774377 1.3801417281733854 chr19 59128983 6332666 0.10709918687422715 2.337884396344921 chr20 63025520 6354802 0.10082902925672013 0.4981754647002912 chr21 48129895 4092289 0.08502592827181527 0.4642303859690106 chr22 51304566 3503128 0.0682810181066535 0.38744127798779465 chrMT 16571 231836 13.990465270653551 8.45941032125284 chrX 155270560 16400412 0.1056247365888292 0.5539218082552407 chrY 59373566 993650 0.016735562084985767 0.9966139903276038