BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716387.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 = 1,205,927 number of mapped reads = 1,070,802 (88.79%) number of supplementary alignments = 4,638 (0.38%) number of secondary alignments = 0 number of mapped bases = 61,054,921 bp number of sequenced bases = 61,035,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,193 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.208 >>>>>>> ACTG content number of A's = 14,945,255 bp (24.49%) number of C's = 12,399,412 bp (20.31%) number of T's = 18,684,734 bp (30.61%) number of G's = 15,005,952 bp (24.59%) number of N's = 518 bp (0%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 325,471 number of insertions = 4,415 mapped reads with insertion percentage = 0.41% number of deletions = 11,847 mapped reads with deletion percentage = 1.1% homopolymer indels = 38.83% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.187X There is a 1.83% of reference with a coverageData >= 1X There is a 0.1% 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 5169568 0.020740441806161036 0.2474054522951663 chr2 243199373 4760779 0.019575622014453137 0.24442639514122402 chr3 198022430 3458470 0.01746504171269891 0.1422910478461218 chr4 191154276 3777547 0.019761770853611457 0.16379502337048213 chr5 180915260 3419605 0.018901694638694382 0.144243606922663 chr6 171115067 3212572 0.01877433738783505 0.16218281393424602 chr7 159138663 3488637 0.0219219951596552 0.24446278313384448 chr8 146364022 3150262 0.021523472482875606 0.18461132611728007 chr9 141213431 2027009 0.01435422243936556 0.1406745213611409 chr10 135534747 2752300 0.020306969695380032 0.24735465294706654 chr11 135006516 2160751 0.016004790465076517 0.1547771725468104 chr12 133851895 3039270 0.022706215702063836 0.16007636668257869 chr13 115169878 1800900 0.01563690116959228 0.13154111759366982 chr14 107349540 2041377 0.01901616904925722 0.15018253367268025 chr15 102531392 2250231 0.021946751683620955 0.15813644866019463 chr16 90354753 2156488 0.02386690161169496 0.17655170377148033 chr17 81195210 2718909 0.033486076333813286 0.20180922060832374 chr18 78077248 1141890 0.014625131254626188 0.20938485396852072 chr19 59128983 1681576 0.02843911589008727 0.23611413661989275 chr20 63025520 1994782 0.03165038543117137 0.1958402806256663 chr21 48129895 760838 0.015808012878482283 0.1415426782257743 chr22 51304566 566778 0.011047320817410286 0.11096533298129098 chrMT 16571 4479 0.2702914730553376 0.5742426850094787 chrX 155270560 3313792 0.02134204964547046 0.1622265255676242 chrY 59373566 206111 0.003471426998337947 0.11651940612042609