BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525165.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 = 2,402,054 number of mapped reads = 2,201,873 (91.67%) number of supplementary alignments = 6,770 (0.28%) number of secondary alignments = 0 number of mapped bases = 127,196,526 bp number of sequenced bases = 127,156,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,481 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8334 >>>>>>> ACTG content number of A's = 29,871,022 bp (23.49%) number of C's = 23,332,337 bp (18.35%) number of T's = 41,326,985 bp (32.5%) number of G's = 32,623,853 bp (25.66%) number of N's = 2,656 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 659,295 number of insertions = 8,147 mapped reads with insertion percentage = 0.37% number of deletions = 24,827 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0411X std coverageData = 0.3689X There is a 3.6% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 13839485 0.05552437520306118 0.6652551028478011 chr2 243199373 10910401 0.04486196187685073 0.5546125219616175 chr3 198022430 10157377 0.05129407310070885 0.2573354999544409 chr4 191154276 7180521 0.037564009292682526 0.23228704923963908 chr5 180915260 5863070 0.03240782452513956 0.2016955473667257 chr6 171115067 6431743 0.03758723946851507 0.2656314258427181 chr7 159138663 7622321 0.04789735477418206 0.5490963294764158 chr8 146364022 6029228 0.041193374694226424 0.30910585409819014 chr9 141213431 4351259 0.03081335089153099 0.2609373783812287 chr10 135534747 7046095 0.05198736970380002 0.4092814162356451 chr11 135006516 5914091 0.043805967113468805 0.3088265289270204 chr12 133851895 5967023 0.04457929415194309 0.2399870982452295 chr13 115169878 3985294 0.03460361397621694 0.21161216292560883 chr14 107349540 4836240 0.04505133417432436 0.24523095885228724 chr15 102531392 3574669 0.034864141901048216 0.21227816803307673 chr16 90354753 3533796 0.03911023917026257 0.2503434993784764 chr17 81195210 2671322 0.03289999496275704 0.21269497493916176 chr18 78077248 2720524 0.034844004747708324 0.5047634914010162 chr19 59128983 2409086 0.04074289591620407 0.4591349541080691 chr20 63025520 2423988 0.038460420477292374 0.22457156539677572 chr21 48129895 1652015 0.034324093164965354 0.2221529068143544 chr22 51304566 1070166 0.020859079092492468 0.1599065656707026 chrMT 16571 119835 7.231609438175125 4.516115441741889 chrX 155270560 6510279 0.041928611579683875 0.25732843496518426 chrY 59373566 376698 0.006344540599094216 0.1761403505765827