BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524686.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 = 2,026,902 number of mapped reads = 1,884,360 (92.97%) number of supplementary alignments = 8,287 (0.41%) number of secondary alignments = 0 number of mapped bases = 112,636,078 bp number of sequenced bases = 112,601,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,293 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.091 >>>>>>> ACTG content number of A's = 29,713,095 bp (26.39%) number of C's = 23,194,159 bp (20.6%) number of T's = 33,920,505 bp (30.12%) number of G's = 25,757,752 bp (22.88%) number of N's = 15,945 bp (0.01%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 553,664 number of insertions = 8,769 mapped reads with insertion percentage = 0.46% number of deletions = 21,676 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.89% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.3336X There is a 3.23% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9066565 0.036375295530356976 0.6132971472742558 chr2 243199373 9511829 0.039111239813928306 0.43847700656576394 chr3 198022430 7475311 0.0377498195532698 0.21344302886491684 chr4 191154276 7299945 0.03818876120772731 0.24973344231032354 chr5 180915260 6841952 0.03781854554447204 0.21473124463216184 chr6 171115067 6402674 0.03741735962970461 0.2417344752840575 chr7 159138663 6194673 0.038926260176007636 0.38115754840181515 chr8 146364022 5732986 0.03916936636245211 0.3720468864530298 chr9 141213431 4737287 0.03354700021416518 0.2763220750554656 chr10 135534747 5529269 0.04079595175693212 0.3571026892204178 chr11 135006516 5141930 0.03808653206042292 0.28650275691663574 chr12 133851895 5036172 0.037624958540930634 0.2154225410289814 chr13 115169878 3525658 0.030612674609241143 0.1920139051494907 chr14 107349540 3337215 0.031087371217426735 0.2014528875892714 chr15 102531392 3227146 0.03147471166684248 0.19465948559898041 chr16 90354753 3265981 0.036146200300055054 0.22841520353872105 chr17 81195210 3024301 0.03724728342965059 0.22766473302816534 chr18 78077248 3012100 0.038578460142447646 0.5235923436095686 chr19 59128983 2322428 0.03927732022720567 0.4590351120679333 chr20 63025520 2370085 0.037605163749541454 0.21758163925181834 chr21 48129895 1514053 0.031457641866868814 0.23200738689331796 chr22 51304566 1345415 0.02622407915895829 0.1780638714546257 chrMT 16571 50269 3.0335525918773762 2.3411049806335833 chrX 155270560 6279497 0.04044228989706741 0.2436185217449645 chrY 59373566 391337 0.006591098132795325 0.25953671897104574