BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231844.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 = 1,252,351 number of mapped reads = 613,888 (49.02%) number of supplementary alignments = 4,844 (0.39%) number of secondary alignments = 0 number of mapped bases = 39,248,322 bp number of sequenced bases = 39,234,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,776 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0961 >>>>>>> ACTG content number of A's = 11,058,688 bp (28.19%) number of C's = 7,950,497 bp (20.26%) number of T's = 10,886,644 bp (27.75%) number of G's = 9,335,354 bp (23.79%) number of N's = 3,029 bp (0.01%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 253,526 number of insertions = 2,858 mapped reads with insertion percentage = 0.46% number of deletions = 8,543 mapped reads with deletion percentage = 1.38% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 1.7104X There is a 1.16% of reference with a coverageData >= 1X There is a 0.05% 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 3308315 0.013273046168258092 0.324020559280823 chr2 243199373 3450276 0.014187026707507178 6.074665262043049 chr3 198022430 3592831 0.01814355575779976 0.13965191380630412 chr4 191154276 971977 0.005084777700709138 0.07747147326586286 chr5 180915260 2103617 0.011627637160071517 0.11311698272724054 chr6 171115067 2720309 0.01589754220766544 0.15023449769878938 chr7 159138663 2863251 0.017992177048766583 0.2533301627189699 chr8 146364022 2438718 0.016662004546445165 0.15953914518318468 chr9 141213431 1764620 0.012496120145965435 0.14641364895626155 chr10 135534747 1737984 0.012823161871545752 0.1491618592824594 chr11 135006516 1596623 0.01182626622258736 0.1452116586546676 chr12 133851895 1274299 0.009520216355547301 0.10449832707946044 chr13 115169878 1369167 0.011888238693801517 0.11314661720017398 chr14 107349540 1841987 0.01715877869621053 0.14732720612557507 chr15 102531392 857598 0.008364248092915777 0.0961920736092727 chr16 90354753 1011117 0.011190523646276804 0.12051639398669395 chr17 81195210 982660 0.012102438062540882 0.11945686130824852 chr18 78077248 771390 0.009879830805511998 0.26886001378206065 chr19 59128983 1363273 0.023055918279534758 0.24117597848864541 chr20 63025520 908444 0.014413907255346723 0.1303812130281851 chr21 48129895 807034 0.016767832134269148 0.13756375376776908 chr22 51304566 402305 0.007841504789261837 0.09141012015888078 chrMT 16571 13574 0.8191418743588196 1.0046324134750917 chrX 155270560 1013805 0.0065292802447547045 0.09486358186046473 chrY 59373566 83148 0.001400421190804002 0.045996025541493804