BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525179.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 = 4,102,758 number of mapped reads = 3,734,584 (91.03%) number of supplementary alignments = 12,721 (0.31%) number of secondary alignments = 0 number of mapped bases = 215,833,897 bp number of sequenced bases = 215,765,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,394 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5717 >>>>>>> ACTG content number of A's = 54,365,801 bp (25.2%) number of C's = 41,268,140 bp (19.13%) number of T's = 68,522,595 bp (31.76%) number of G's = 51,604,118 bp (23.92%) number of N's = 5,225 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,115,678 number of insertions = 12,450 mapped reads with insertion percentage = 0.33% number of deletions = 42,555 mapped reads with deletion percentage = 1.13% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0697X std coverageData = 0.6261X There is a 5.71% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 22589259 0.0906286969692244 1.1575257705308044 chr2 243199373 17796776 0.07317772155605023 0.9540920760325791 chr3 198022430 16435477 0.08299805734128199 0.35026039131803877 chr4 191154276 11916944 0.062342021582609014 0.3325602718579359 chr5 180915260 9576548 0.05293388739015161 0.2770668814783534 chr6 171115067 13415639 0.07840127251915227 0.40299679783796716 chr7 159138663 15710890 0.09872453182543076 1.1573405760728053 chr8 146364022 12075168 0.0825009304540702 0.525395656854114 chr9 141213431 7148720 0.0506235132832372 0.4250562555785242 chr10 135534747 11408056 0.08417071085099675 0.6392868265601463 chr11 135006516 9677289 0.07168016245971416 0.45776542367821604 chr12 133851895 9557563 0.07140401710412841 0.3278911934177528 chr13 115169878 6510556 0.05653002428291189 0.2925870065916753 chr14 107349540 7851871 0.07314303349599821 0.3410117264167808 chr15 102531392 5841607 0.05697383880246159 0.30240193943759475 chr16 90354753 7562715 0.08370024540933668 0.4122589668239592 chr17 81195210 3909893 0.04815423225089263 0.28651957455450916 chr18 78077248 4484901 0.05744184272478456 0.834758704790752 chr19 59128983 3850006 0.06511199423132308 0.8289162540310291 chr20 63025520 4566721 0.07245828356513362 0.33428816530232536 chr21 48129895 2718643 0.05648553773075964 0.3071818839314498 chr22 51304566 1710527 0.03334063872599566 0.21614008452132435 chrMT 16571 316793 19.11731337879428 11.300751037562588 chrX 155270560 8600125 0.05538799499402849 0.3385513473958874 chrY 59373566 601210 0.010125886661414273 0.26608942434997945