BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238051.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 = 2,011,806 number of mapped reads = 1,762,230 (87.59%) number of supplementary alignments = 20,600 (1.02%) number of secondary alignments = 0 number of mapped bases = 117,185,396 bp number of sequenced bases = 117,126,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,082 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9494 >>>>>>> ACTG content number of A's = 31,985,020 bp (27.31%) number of C's = 22,218,640 bp (18.97%) number of T's = 36,622,235 bp (31.27%) number of G's = 26,284,230 bp (22.44%) number of N's = 16,105 bp (0.01%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 915,419 number of insertions = 8,017 mapped reads with insertion percentage = 0.45% number of deletions = 33,222 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0379X std coverageData = 0.4052X There is a 2.71% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7021551 0.028170645962001434 0.6981226556370014 chr2 243199373 15443210 0.06350020482988664 0.5237304697997425 chr3 198022430 6370333 0.03216975470910038 0.2358798539783118 chr4 191154276 6331872 0.03312440680113272 0.2581401384435535 chr5 180915260 10529605 0.05820186202092626 0.32068331463171684 chr6 171115067 2469071 0.014429302125685986 0.18694991069276207 chr7 159138663 11343238 0.07127895752146667 0.7227193735493741 chr8 146364022 1834149 0.012531419777464164 0.410389523812544 chr9 141213431 6655529 0.04713099138565651 0.37726049861846495 chr10 135534747 3455998 0.025498981453073433 0.33915134325927004 chr11 135006516 8161301 0.0604511637053133 0.4462437504804325 chr12 133851895 4265904 0.03187032951606699 0.24149921630657437 chr13 115169878 6371742 0.05532472648794505 0.31117165913742173 chr14 107349540 1677945 0.01563066781655515 0.1890479400842016 chr15 102531392 1849088 0.018034359662258366 0.17431501015383105 chr16 90354753 6453814 0.07142749867292537 0.3747591941533344 chr17 81195210 3160462 0.03892424195959343 0.3001331209950149 chr18 78077248 3818574 0.048907640802093845 0.4801806284489384 chr19 59128983 1865862 0.03155579388199523 0.557498465315926 chr20 63025520 2691472 0.04270447907450823 0.2809801238607799 chr21 48129895 1351501 0.028080281496562585 0.2439354354639577 chr22 51304566 719661 0.014027231026571788 0.15605715103125406 chrMT 16571 69032 4.165831874962284 3.469969696797099 chrX 155270560 3027855 0.019500509304532683 0.21686293130261344 chrY 59373566 246627 0.004153818216005419 0.13277050423473663