BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117300.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 465,924 number of mapped reads = 439,591 (94.35%) number of supplementary alignments = 2,915 (0.63%) number of secondary alignments = 0 number of mapped bases = 99,584,813 bp number of sequenced bases = 99,366,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,245 duplication rate = 18.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.5561 >>>>>>> ACTG content number of A's = 28,391,556 bp (28.57%) number of C's = 21,021,020 bp (21.16%) number of T's = 29,439,913 bp (29.63%) number of G's = 20,514,019 bp (20.64%) number of N's = 0 bp (0%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 549,363 number of insertions = 782,517 mapped reads with insertion percentage = 65.02% number of deletions = 181,172 mapped reads with deletion percentage = 28.08% homopolymer indels = 26.42% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.5895X There is a 2.31% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7959251 0.031932722847659425 1.8102928399216114 chr2 243199373 9675274 0.03978330157948228 0.2743600249617484 chr3 198022430 7708465 0.03892723162724546 0.2700193066953483 chr4 191154276 6681335 0.03495257935009521 0.2569296712353966 chr5 180915260 6425175 0.03551483163996227 0.25226380830785766 chr6 171115067 6031705 0.035249409100836224 0.2530592456056924 chr7 159138663 5305510 0.033338912744290176 0.7256184332285386 chr8 146364022 5076131 0.034681548994328674 0.25393288491922805 chr9 141213431 4139170 0.029311447011014128 0.23308614518309384 chr10 135534747 4787722 0.035324683197291096 0.2916343841326367 chr11 135006516 4519616 0.033477021212813166 0.2476510273452922 chr12 133851895 2906394 0.0217135065588724 0.19061667688789236 chr13 115169878 3393008 0.029460897753143405 0.23098358954379858 chr14 107349540 3076731 0.02866086803911782 0.2281658387823521 chr15 102531392 2956835 0.028838338603654187 0.22748884307607484 chr16 90354753 2534683 0.02805256963073099 0.2541769184103272 chr17 81195210 2287835 0.02817697004540046 0.23604065561744053 chr18 78077248 2919704 0.03739506802288933 0.28558132414645876 chr19 59128983 1421836 0.02404634627319736 0.45594169656256367 chr20 63025520 2259902 0.035856935412829596 0.26635077424525894 chr21 48129895 1233849 0.02563581325078727 0.23990605687085406 chr22 51304566 1089206 0.021230196158369217 0.207411743159583 chrMT 16571 22694 1.3695009353690182 2.8142145232230766 chrX 155270560 5061304 0.03259667511986818 0.24226629428412738 chrY 59373566 111478 0.0018775695567956959 0.09061698269953158