BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716834.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 = 933,617 number of mapped reads = 823,346 (88.19%) number of supplementary alignments = 4,866 (0.52%) number of secondary alignments = 0 number of mapped bases = 47,746,968 bp number of sequenced bases = 47,733,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,305 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9813 >>>>>>> ACTG content number of A's = 11,928,676 bp (24.99%) number of C's = 9,476,503 bp (19.85%) number of T's = 15,464,988 bp (32.4%) number of G's = 10,863,378 bp (22.76%) number of N's = 329 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 235,896 number of insertions = 3,145 mapped reads with insertion percentage = 0.38% number of deletions = 8,330 mapped reads with deletion percentage = 1% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.16X There is a 1.41% of reference with a coverageData >= 1X There is a 0.11% 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 3871185 0.015531295306181003 0.2049917508858932 chr2 243199373 3658799 0.015044442569348235 0.2054077684686972 chr3 198022430 3245986 0.016392011753416015 0.13826855452105913 chr4 191154276 3069728 0.016058903123883035 0.14794149592192757 chr5 180915260 2931055 0.01620125908671275 0.13711989472682615 chr6 171115067 2821615 0.01648957657247097 0.14849206587426347 chr7 159138663 2676421 0.016818169447609346 0.20538161231686125 chr8 146364022 2483586 0.016968555291545624 0.17564787034347615 chr9 141213431 1984786 0.014055221135445679 0.13752833683108273 chr10 135534747 2339337 0.017260053615623747 0.16949476788373644 chr11 135006516 2213062 0.016392260652071045 0.15219242322880042 chr12 133851895 2202261 0.01645296840959928 0.1385929574033502 chr13 115169878 1486670 0.012908496785939114 0.12227546129364189 chr14 107349540 1433760 0.0133559957499585 0.12692581900919941 chr15 102531392 1438185 0.014026777282025001 0.12949021474731953 chr16 90354753 1449831 0.01604598487475252 0.14063716940968043 chr17 81195210 1221057 0.015038534908647936 0.13628862566593963 chr18 78077248 1298636 0.01663270713639907 0.2048540604464369 chr19 59128983 903723 0.015283925989391699 0.16972081642380235 chr20 63025520 1037037 0.016454239489019685 0.14020375333143933 chr21 48129895 641579 0.013330155821033892 0.1300071747110749 chr22 51304566 455070 0.00886997075464979 0.10166141411165633 chrMT 16571 6431 0.3880876229557661 0.7082690828163285 chrX 155270560 2728125 0.017570136927438144 0.14851575488127247 chrY 59373566 149043 0.002510258521443701 0.0815383429606793