BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524891.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 = 2,614,270 number of mapped reads = 2,414,048 (92.34%) number of supplementary alignments = 8,428 (0.32%) number of secondary alignments = 0 number of mapped bases = 141,126,754 bp number of sequenced bases = 141,084,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,414 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2545 >>>>>>> ACTG content number of A's = 34,416,718 bp (24.39%) number of C's = 24,708,554 bp (17.51%) number of T's = 46,822,313 bp (33.19%) number of G's = 35,118,156 bp (24.89%) number of N's = 18,287 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 690,333 number of insertions = 9,843 mapped reads with insertion percentage = 0.41% number of deletions = 27,177 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.4282X There is a 3.96% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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% 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 11216916 0.045002559893321185 0.8904931007157807 chr2 243199373 11890186 0.04889069348052966 0.4538015349294682 chr3 198022430 9505446 0.04800186524324542 0.2450256033397038 chr4 191154276 9184757 0.04804892253626594 0.2855439946247149 chr5 180915260 8574751 0.04739650486089454 0.24704380279966912 chr6 171115067 8141623 0.04757981364668489 0.28100759091836813 chr7 159138663 7913010 0.04972399447643971 0.5755768274849942 chr8 146364022 7360659 0.05029008426674692 0.4141902777451691 chr9 141213431 5897881 0.04176572269531501 0.3733728854122702 chr10 135534747 6734035 0.04968493429954165 0.3947651534445594 chr11 135006516 6460085 0.0478501719131838 0.36977762143568343 chr12 133851895 6299664 0.047064436405625784 0.252767946345794 chr13 115169878 4479722 0.03889664622202691 0.22047650515596456 chr14 107349540 4315129 0.040196995720708256 0.24420296458014926 chr15 102531392 4038116 0.039384191721497354 0.22163566340494148 chr16 90354753 4018997 0.04448019463901362 0.263096926563692 chr17 81195210 3742278 0.04608988633689105 0.26708498361060956 chr18 78077248 3780688 0.04842240341257929 0.762415760191894 chr19 59128983 2693102 0.0455462256132496 0.5972098912050724 chr20 63025520 3016037 0.047854218418189966 0.25746286080155156 chr21 48129895 1898928 0.03945423109690973 0.2603520990042577 chr22 51304566 1647404 0.03211028039882454 0.19986610278777284 chrMT 16571 26863 1.6210850280610705 1.6887827093753378 chrX 155270560 7870568 0.05068937730372068 0.3102560693439898 chrY 59373566 419909 0.007072322386699832 0.17900061132703823