BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716096.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 = 1,193,226 number of mapped reads = 1,072,843 (89.91%) number of supplementary alignments = 18,451 (1.55%) number of secondary alignments = 0 number of mapped bases = 84,016,832 bp number of sequenced bases = 83,980,514 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,974 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.413 >>>>>>> ACTG content number of A's = 21,066,404 bp (25.08%) number of C's = 15,938,066 bp (18.98%) number of T's = 26,423,312 bp (31.46%) number of G's = 20,547,633 bp (24.47%) number of N's = 5,099 bp (0.01%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 714,058 number of insertions = 7,727 mapped reads with insertion percentage = 0.71% number of deletions = 20,956 mapped reads with deletion percentage = 1.92% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.343X There is a 2.42% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 6629218 0.026596595721219887 0.5514063795360632 chr2 243199373 7310970 0.03006163177896022 0.509384790196918 chr3 198022430 5567916 0.0281176026372366 0.18263712730253875 chr4 191154276 5412915 0.028316996685964796 0.1945917125713184 chr5 180915260 5030683 0.027806847249922422 0.18519906886939994 chr6 171115067 4825533 0.02820051492017357 0.2232552124283683 chr7 159138663 4834841 0.03038130966325889 0.4765995115317964 chr8 146364022 4337964 0.02963818526386218 0.45074389604751347 chr9 141213431 3492178 0.02472978650309828 0.36137078321204974 chr10 135534747 3952984 0.02916583449998988 0.30623944856367763 chr11 135006516 3827903 0.028353468509623638 0.3358512274723318 chr12 133851895 3855903 0.0288072350413866 0.18843479574719857 chr13 115169878 2586850 0.022461168188438994 0.16128236503872345 chr14 107349540 2592984 0.024154588831959596 0.22467066548413628 chr15 102531392 2340349 0.022825682499268127 0.16764112892901206 chr16 90354753 2436966 0.026971088062185285 0.20609608707692986 chr17 81195210 2239116 0.027576946965221224 0.19886984268879648 chr18 78077248 2322783 0.029749806243170866 0.6792181228602077 chr19 59128983 1705367 0.028841473562973338 0.38801898217488084 chr20 63025520 1675017 0.026576805712987372 0.18830122159873566 chr21 48129895 1076786 0.022372498423277258 0.1733029444657342 chr22 51304566 869777 0.016953208414237437 0.14062592778054062 chrMT 16571 8906 0.5374449339207048 0.8953330205480964 chrX 155270560 4851996 0.031248653962476853 0.2649283375385883 chrY 59373566 230927 0.0038893907770336717 0.11881237079084156