BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524646.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 = 2,675,772 number of mapped reads = 2,475,816 (92.53%) number of supplementary alignments = 12,006 (0.45%) number of secondary alignments = 0 number of mapped bases = 144,668,120 bp number of sequenced bases = 144,621,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,718 duplication rate = 6.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9629 >>>>>>> ACTG content number of A's = 37,899,063 bp (26.21%) number of C's = 27,143,734 bp (18.77%) number of T's = 44,122,744 bp (30.51%) number of G's = 35,454,783 bp (24.52%) number of N's = 1,152 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 732,365 number of insertions = 11,148 mapped reads with insertion percentage = 0.45% number of deletions = 27,763 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.2% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.4026X There is a 3.79% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 14830964 0.059502214841021396 0.7479092621044934 chr2 243199373 12812386 0.05268264404612589 0.5107912752367251 chr3 198022430 10294533 0.05198670170848828 0.27293273263251694 chr4 191154276 6679398 0.03494244617368643 0.30942556180584974 chr5 180915260 8854514 0.048942880771914984 0.265029649817825 chr6 171115067 9411560 0.05500135180965683 0.30063013368562613 chr7 159138663 8726936 0.05483856553451125 0.4928314209574486 chr8 146364022 11700722 0.07994261048661262 0.5391248781196143 chr9 141213431 5162107 0.03655535428496175 0.30364710983953397 chr10 135534747 6222841 0.045913252045986404 0.4372932363492562 chr11 135006516 7304135 0.05410209237604502 0.346833237784581 chr12 133851895 4799420 0.035856197627982776 0.2338184042424398 chr13 115169878 3429037 0.02977373128762019 0.20911582151320138 chr14 107349540 2628503 0.024485461232530665 0.1995773010708924 chr15 102531392 3796344 0.03702616268001121 0.23235685580058693 chr16 90354753 4353375 0.04818091860646224 0.28456463108763164 chr17 81195210 3331532 0.04103113964481402 0.2609954776492281 chr18 78077248 3796238 0.04862156514532889 0.5367352668657865 chr19 59128983 2925395 0.049474806627403015 0.5106705840559821 chr20 63025520 2744266 0.043542139755451445 0.2631200399892316 chr21 48129895 1244644 0.025860102125716253 0.2627098381880679 chr22 51304566 2564696 0.04998962470513833 0.26923039999559223 chrMT 16571 27611 1.6662241264860298 1.630550112244122 chrX 155270560 6591647 0.04245265168103986 0.2728071282595768 chrY 59373566 435316 0.007331814969644909 0.2863079920237088