BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525101.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 = 628,230 number of mapped reads = 567,337 (90.31%) number of supplementary alignments = 15,123 (2.41%) number of secondary alignments = 0 number of mapped bases = 43,561,192 bp number of sequenced bases = 43,544,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,325 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.165 >>>>>>> ACTG content number of A's = 11,362,145 bp (26.09%) number of C's = 8,107,904 bp (18.62%) number of T's = 13,797,165 bp (31.69%) number of G's = 10,275,795 bp (23.6%) number of N's = 1,454 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 325,192 number of insertions = 3,704 mapped reads with insertion percentage = 0.65% number of deletions = 9,858 mapped reads with deletion percentage = 1.71% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1856X There is a 1.31% of reference with a coverageData >= 1X There is a 0.06% 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 4364604 0.017510905218567137 0.32949137228260345 chr2 243199373 3735843 0.01536123614923958 0.22617037663525624 chr3 198022430 2887454 0.014581449182297177 0.12558755577950073 chr4 191154276 2818031 0.014742181336294041 0.12905740483985437 chr5 180915260 2630081 0.01453764044006017 0.12673001235353845 chr6 171115067 2537562 0.014829564949999405 0.13560806253201754 chr7 159138663 2408703 0.015135875560296747 0.23937872062341153 chr8 146364022 1234327 0.008433267842284356 0.20239993620708996 chr9 141213431 1791638 0.01268744755589148 0.17515008021397077 chr10 135534747 2039061 0.015044562705385062 0.18623400218011155 chr11 135006516 2441048 0.01808096432915875 0.21669252835256914 chr12 133851895 1941861 0.014507534615031039 0.12570849520123595 chr13 115169878 1607263 0.013955584810118493 0.12278565410776901 chr14 107349540 1297798 0.012089460280873118 0.12576826943991143 chr15 102531392 1195009 0.011655054873340644 0.11152030472287229 chr16 90354753 930748 0.010301040831797748 0.11199828851032319 chr17 81195210 1265093 0.015580882172729155 0.14208006566421627 chr18 78077248 1190027 0.015241661693813798 0.27888143709503044 chr19 59128983 804944 0.013613357767374419 0.21503228161697982 chr20 63025520 836579 0.013273654862347824 0.1218579656670387 chr21 48129895 566079 0.01176148420851531 0.11690700778810327 chr22 51304566 423569 0.008255970823337634 0.09399311786926547 chrMT 16571 1048 0.0632430149055579 0.28980226907559703 chrX 155270560 2512519 0.016181554313966538 0.1547181661820464 chrY 59373566 100303 0.0016893544847887357 0.05002881047014001