BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174087.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 = 1,422,926 number of mapped reads = 1,391,232 (97.77%) number of supplementary alignments = 138,025 (9.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 696,106 number of mapped paired reads (second in pair) = 695,126 number of mapped paired reads (both in pair) = 1,370,646 number of mapped paired reads (singletons) = 20,586 number of mapped bases = 164,659,137 bp number of sequenced bases = 164,553,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,047,005 duplication rate = 63.02% >>>>>>> Insert size mean insert size = 1,017,327.8627 std insert size = 9,559,868.112 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.9528 >>>>>>> ACTG content number of A's = 49,611,289 bp (30.15%) number of C's = 32,133,194 bp (19.53%) number of T's = 49,482,556 bp (30.07%) number of G's = 33,324,640 bp (20.25%) number of N's = 1,792 bp (0%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,675,058 number of insertions = 19,201 mapped reads with insertion percentage = 1.33% number of deletions = 41,559 mapped reads with deletion percentage = 2.92% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.9356X There is a 1.23% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.19% 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 0.07% 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 13211187 0.05300362722065194 0.7417718618762477 chr2 243199373 14884529 0.06120299084817131 2.316562090240055 chr3 198022430 11194403 0.05653098489903391 0.6663509067586881 chr4 191154276 11455421 0.05992762097563541 0.7640716326700093 chr5 180915260 10206578 0.05641634652599233 0.6560415699650336 chr6 171115067 9884244 0.05776372690781227 0.699591989396003 chr7 159138663 9148112 0.05748516311212191 0.7649526129642724 chr8 146364022 8560266 0.05848613534274154 0.8103220910282147 chr9 141213431 7017016 0.04969085412279233 0.726020488628504 chr10 135534747 8422554 0.06214313440965806 0.8853892223698168 chr11 135006516 7391066 0.05474599463036288 0.6570668328839369 chr12 133851895 7467201 0.05578703984728793 0.6617850194554822 chr13 115169878 5576112 0.048416409714352564 0.6129296323421072 chr14 107349540 5072851 0.04725545167683066 0.6092416890332907 chr15 102531392 4560363 0.04447772444170074 0.5779474064952903 chr16 90354753 5074254 0.05615923713498503 0.6970433599961929 chr17 81195210 4268051 0.0525653052686236 0.6452010496457103 chr18 78077248 4826939 0.061822606759910394 0.9696505526615047 chr19 59128983 2827606 0.047820981463523565 0.6253087785874504 chr20 63025520 3525874 0.0559435923733751 0.658222411572746 chr21 48129895 2271366 0.04719241544158781 0.6699148665508349 chr22 51304566 1878484 0.03661436293993794 0.535026802904369 chrMT 16571 422363 25.488081588316938 21.970683715343377 chrX 155270560 4278423 0.02755463109040117 0.45622550088887437 chrY 59373566 1233874 0.020781537696422006 0.4669426480211005