BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524733.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 = 1,647,393 number of mapped reads = 1,515,296 (91.98%) number of supplementary alignments = 6,026 (0.37%) number of secondary alignments = 0 number of mapped bases = 88,300,885 bp number of sequenced bases = 88,270,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,680 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.316 >>>>>>> ACTG content number of A's = 22,143,126 bp (25.09%) number of C's = 16,860,479 bp (19.1%) number of T's = 28,159,528 bp (31.9%) number of G's = 21,105,279 bp (23.91%) number of N's = 1,875 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 442,957 number of insertions = 5,924 mapped reads with insertion percentage = 0.39% number of deletions = 19,104 mapped reads with deletion percentage = 1.25% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2779X There is a 2.59% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 10005281 0.040141448634545225 0.49522478986309604 chr2 243199373 7433457 0.030565280281376384 0.34799642261510166 chr3 198022430 7107404 0.035891913860465204 0.20393586732733607 chr4 191154276 5056783 0.026453936086682152 0.18668897314566385 chr5 180915260 3822587 0.021129157374563095 0.15770163445499247 chr6 171115067 5396232 0.031535691710888325 0.21437505204494345 chr7 159138663 6011838 0.037777356468050756 0.4670073759758073 chr8 146364022 4828615 0.032990450344415924 0.295696763370277 chr9 141213431 2826459 0.020015511130807382 0.20049314622504905 chr10 135534747 4525376 0.03338904672172369 0.2830860689832948 chr11 135006516 3863817 0.028619485299509542 0.2211621997243973 chr12 133851895 3970867 0.02966612463723431 0.18727849101618996 chr13 115169878 2667772 0.023163799826201082 0.16504498848410418 chr14 107349540 3514848 0.0327420872040998 0.19987938727724272 chr15 102531392 1614425 0.015745665483601352 0.13693446301075762 chr16 90354753 2293023 0.025378000867314638 0.18866448977754147 chr17 81195210 1668574 0.020550153143270397 0.15920986939514564 chr18 78077248 1798792 0.023038619393962245 0.36820049001853783 chr19 59128983 1436277 0.024290575063670553 0.35396555180011785 chr20 63025520 1518986 0.024101126020062983 0.1702366528205739 chr21 48129895 1109820 0.023058849390799628 0.17259710451184002 chr22 51304566 728078 0.014191290498393457 0.12692513127441524 chrMT 16571 147937 8.927463641301069 5.518591276740638 chrX 155270560 4693354 0.03022694063832835 0.2022164373256638 chrY 59373566 260283 0.00438381956037473 0.12186650822309525