BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716309.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 = 1,134,741 number of mapped reads = 1,047,040 (92.27%) number of supplementary alignments = 3,775 (0.33%) number of secondary alignments = 0 number of mapped bases = 61,033,881 bp number of sequenced bases = 61,013,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,321 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9189 >>>>>>> ACTG content number of A's = 15,423,918 bp (25.28%) number of C's = 11,943,248 bp (19.57%) number of T's = 19,172,810 bp (31.42%) number of G's = 14,472,512 bp (23.72%) number of N's = 1,300 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 307,258 number of insertions = 5,278 mapped reads with insertion percentage = 0.5% number of deletions = 12,402 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2071X There is a 1.8% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5150334 0.020663274495913892 0.294086281558206 chr2 243199373 4761315 0.019577825967503626 0.29469542302378954 chr3 198022430 3457132 0.017458284902371918 0.14053166059138236 chr4 191154276 3717319 0.01944669550578089 0.18718776595992018 chr5 180915260 3467323 0.01916545348358121 0.1485083683130649 chr6 171115067 3226827 0.018857643903444226 0.16472323146523402 chr7 159138663 3393142 0.02132192099665937 0.23851948452617133 chr8 146364022 3205318 0.021899630497992192 0.27334855664619384 chr9 141213431 2014713 0.014267148568892147 0.1510904834758135 chr10 135534747 2699569 0.019917910792278233 0.23842562978747034 chr11 135006516 2181485 0.016158368237574546 0.16668280198195173 chr12 133851895 3006431 0.02246087737495237 0.16147940994078974 chr13 115169878 1814082 0.015751358180652063 0.1340202397569151 chr14 107349540 2065275 0.019238787609150446 0.1499687942502224 chr15 102531392 2267994 0.022119996186143655 0.1582734525921889 chr16 90354753 2125365 0.023522448232468744 0.17028018068032086 chr17 81195210 2714976 0.033437637515809124 0.20376086734633825 chr18 78077248 1133375 0.014516072595181633 0.2274816520214525 chr19 59128983 1611263 0.027249969782162497 0.24619472751258004 chr20 63025520 2065261 0.0327686467323078 0.20202321497682454 chr21 48129895 803486 0.0166941149570345 0.1736952466932873 chr22 51304566 583072 0.011364914382084432 0.11433192648043591 chrMT 16571 68282 4.120572083760787 3.3335054032563893 chrX 155270560 3242976 0.02088596833810608 0.16294340092739756 chrY 59373566 257566 0.0043380584551717845 0.21031012727826817