BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524887.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 = 2,489,502 number of mapped reads = 2,295,109 (92.19%) number of supplementary alignments = 9,080 (0.36%) number of secondary alignments = 0 number of mapped bases = 134,167,808 bp number of sequenced bases = 134,127,330 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,025 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1072 >>>>>>> ACTG content number of A's = 33,654,690 bp (25.09%) number of C's = 25,910,428 bp (19.32%) number of T's = 42,077,225 bp (31.37%) number of G's = 32,466,832 bp (24.21%) number of N's = 18,155 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 657,664 number of insertions = 7,902 mapped reads with insertion percentage = 0.34% number of deletions = 25,340 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.4079X There is a 3.79% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10767685 0.04320023339079263 0.8344796711599198 chr2 243199373 11446380 0.04706582857843141 0.44670703929560485 chr3 198022430 8961588 0.045255418792709494 0.23688272173975847 chr4 191154276 8647950 0.04524068297588069 0.2655194924891249 chr5 180915260 8196636 0.045306493216769 0.23982036651784594 chr6 171115067 7589976 0.04435597713905579 0.2628254351430906 chr7 159138663 7374349 0.046339141356239746 0.5788332567437349 chr8 146364022 6985788 0.04772886058023194 0.3878415812551733 chr9 141213431 5646049 0.039982379579744085 0.3576505555631862 chr10 135534747 6391231 0.04715566407483684 0.38061516492468295 chr11 135006516 6096989 0.04516070172494489 0.3571176290265112 chr12 133851895 6045239 0.045163641500929066 0.24503594215477273 chr13 115169878 4212793 0.03657894818643465 0.21246188752947967 chr14 107349540 4031815 0.03755782279085686 0.22916900422043987 chr15 102531392 3839402 0.03744611211364418 0.21679249723997446 chr16 90354753 3859403 0.04271389021449707 0.2582489576190032 chr17 81195210 3610984 0.0444728697665786 0.2614225849831869 chr18 78077248 3561085 0.0456097658565015 0.7094222792503356 chr19 59128983 2679409 0.04531464713336943 0.5348762958146566 chr20 63025520 2835106 0.04498346066799608 0.24251858831578996 chr21 48129895 1795092 0.03729681936767159 0.2472974758219199 chr22 51304566 1584549 0.030885145778252954 0.19561383297912288 chrMT 16571 42831 2.584696155935067 2.0510167818132876 chrX 155270560 7565593 0.04872522518112899 0.2972987826270494 chrY 59373566 399886 0.006735084768194654 0.17294767583671267