BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716991.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 = 2,437,153 number of mapped reads = 2,097,114 (86.05%) number of supplementary alignments = 8,835 (0.36%) number of secondary alignments = 0 number of mapped bases = 118,759,994 bp number of sequenced bases = 118,726,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,864 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1054 >>>>>>> ACTG content number of A's = 29,556,681 bp (24.89%) number of C's = 24,954,951 bp (21.02%) number of T's = 35,211,949 bp (29.66%) number of G's = 29,001,498 bp (24.43%) number of N's = 1,813 bp (0%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 617,525 number of insertions = 8,341 mapped reads with insertion percentage = 0.4% number of deletions = 20,937 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3423X There is a 3.37% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 9720529 0.038999016174968724 0.4340901293401834 chr2 243199373 11434735 0.047017946053668484 0.43363025003646494 chr3 198022430 8904379 0.04496651717686729 0.2575016885778687 chr4 191154276 6589789 0.034473667750963624 0.21458507088644263 chr5 180915260 6751432 0.037318200797434115 0.21399362024957605 chr6 171115067 6547284 0.03826246346851502 0.24522711324571692 chr7 159138663 7370144 0.0463127178591415 0.8140139901314792 chr8 146364022 9169657 0.06264966536653387 0.3276113746659634 chr9 141213431 4923708 0.03486713668192086 0.2464683762980652 chr10 135534747 5565170 0.041060835860784836 0.43820207222942803 chr11 135006516 3933344 0.02913447525747572 0.23095942152664414 chr12 133851895 5575481 0.04165410583092604 0.2431863471345882 chr13 115169878 2182653 0.01895159600672669 0.15151721638062812 chr14 107349540 2978436 0.027745214371668478 0.19769879409178182 chr15 102531392 2846990 0.027767008176383678 0.1874095561550464 chr16 90354753 3709445 0.041054232088930616 0.23772696500350096 chr17 81195210 5096283 0.06276580847564776 0.29562926071388995 chr18 78077248 2725087 0.03490244686902899 0.34659553920758074 chr19 59128983 2560527 0.0433040933580745 0.4286283654892656 chr20 63025520 2658912 0.04218786294821526 0.23517797492279455 chr21 48129895 1212797 0.02519841358473772 0.18554388292305302 chr22 51304566 1776147 0.03461966718517802 0.2093653579465718 chrMT 16571 27835 1.67974171745821 1.652187800619373 chrX 155270560 4253876 0.027396539305326137 0.21630107371435575 chrY 59373566 245354 0.00413237769818306 0.09566256671149265