BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524439.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 = 1,092,561 number of mapped reads = 1,002,213 (91.73%) number of supplementary alignments = 3,721 (0.34%) number of secondary alignments = 0 number of mapped bases = 58,667,432 bp number of sequenced bases = 58,650,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,621 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8403 >>>>>>> ACTG content number of A's = 13,781,356 bp (23.5%) number of C's = 11,835,399 bp (20.18%) number of T's = 18,028,284 bp (30.74%) number of G's = 15,000,075 bp (25.58%) number of N's = 5,877 bp (0.01%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 300,702 number of insertions = 3,597 mapped reads with insertion percentage = 0.36% number of deletions = 10,191 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.2174X There is a 1.71% of reference with a coverageData >= 1X There is a 0.13% 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 4730662 0.01897953947324368 0.4244690339434201 chr2 243199373 4880150 0.02006645798383699 0.2604498489683099 chr3 198022430 3884926 0.019618615931538665 0.15108628549987146 chr4 191154276 3710222 0.019409568426290397 0.18707194352536818 chr5 180915260 3520261 0.01945806561591322 0.15015577237859262 chr6 171115067 3288612 0.0192187167246938 0.16163310234491482 chr7 159138663 3025077 0.01900906381248157 0.24339515092041908 chr8 146364022 2827449 0.01931792363563226 0.17321189020616246 chr9 141213431 2452746 0.017369070226754848 0.17042089237263303 chr10 135534747 2912271 0.02148726481187883 0.2336075074397614 chr11 135006516 2709474 0.020069209103951692 0.18552682519232494 chr12 133851895 2701412 0.02018209753399457 0.15756303843712902 chr13 115169878 1825738 0.015852565199383124 0.13669435341990746 chr14 107349540 1740571 0.016214051778889783 0.14080101250656107 chr15 102531392 1725421 0.016828221741103447 0.14013812756973892 chr16 90354753 1837530 0.020336838284533854 0.16329325639526168 chr17 81195210 1675507 0.020635539953649976 0.16479810184356286 chr18 78077248 1585554 0.020307503666112822 0.2938681748555463 chr19 59128983 1327519 0.022451240198059892 0.2915423326037906 chr20 63025520 1278571 0.020286560110888415 0.15807953685512893 chr21 48129895 809807 0.016825447053229598 0.16741524048678183 chr22 51304566 768751 0.014984065940641618 0.13400174331098025 chrMT 16571 8550 0.5159616196970611 0.8227986726039209 chrX 155270560 3219379 0.020733994905408983 0.16634585957813555 chrY 59373566 221272 0.0037267763233220655 0.13330965019506688