BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173904.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,275,998 number of mapped reads = 1,246,751 (97.71%) number of supplementary alignments = 118,123 (9.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 623,716 number of mapped paired reads (second in pair) = 623,035 number of mapped paired reads (both in pair) = 1,227,618 number of mapped paired reads (singletons) = 19,133 number of mapped bases = 148,337,618 bp number of sequenced bases = 148,248,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 952,596 duplication rate = 64.04% >>>>>>> Insert size mean insert size = 1,133,612.4462 std insert size = 9,603,805.3947 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.1198 >>>>>>> ACTG content number of A's = 44,454,171 bp (29.99%) number of C's = 29,222,422 bp (19.71%) number of T's = 44,331,671 bp (29.9%) number of G's = 30,238,986 bp (20.4%) number of N's = 1,643 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 1,534,317 number of insertions = 16,699 mapped reads with insertion percentage = 1.29% number of deletions = 35,573 mapped reads with deletion percentage = 2.79% homopolymer indels = 42.95% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.8601X There is a 1.06% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 12057582 0.048375333837182295 0.7061978933806133 chr2 243199373 13613769 0.05597781290332521 2.060242181800779 chr3 198022430 10221705 0.051618925189434346 0.6454690765341015 chr4 191154276 10153022 0.05311428136716126 0.7193873120050691 chr5 180915260 9213406 0.05092663825041625 0.6396064361824537 chr6 171115067 8490058 0.04961607501226061 0.6487186831501978 chr7 159138663 8014851 0.05036394581246419 0.6896884516707786 chr8 146364022 7327882 0.05006614262075963 0.7407268105083279 chr9 141213431 6150354 0.0435536050391694 0.6681698464779126 chr10 135534747 7299583 0.053857650245217194 0.8316611393961504 chr11 135006516 6884663 0.050995042342993284 0.6343910119532563 chr12 133851895 6852148 0.051192013381655896 0.6315565839788572 chr13 115169878 4813895 0.041798212202673345 0.5754091971948869 chr14 107349540 4449266 0.041446530651179314 0.5748561000565866 chr15 102531392 4165062 0.040622310092113055 0.5605253940833007 chr16 90354753 4860705 0.05379578648175819 0.728800596249058 chr17 81195210 4150111 0.051112756528371564 0.670829956959537 chr18 78077248 4057695 0.051970261554300685 0.8784406189136568 chr19 59128983 2778019 0.046982357196977326 0.6549404179805521 chr20 63025520 3119938 0.04950277284503166 0.614460354775782 chr21 48129895 2142110 0.044506849640956 0.6409905760785308 chr22 51304566 1835111 0.03576896060284381 0.5162585836518265 chrMT 16571 208347 12.572988956610947 15.684818093236778 chrX 155270560 4186295 0.026961292597901365 0.46162930692900705 chrY 59373566 1292041 0.021761216094044276 0.4598972878173054