BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524664.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 = 1,737,957 number of mapped reads = 1,605,252 (92.36%) number of supplementary alignments = 7,320 (0.42%) number of secondary alignments = 0 number of mapped bases = 94,348,150 bp number of sequenced bases = 94,320,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,378 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5787 >>>>>>> ACTG content number of A's = 23,440,405 bp (24.85%) number of C's = 16,887,978 bp (17.9%) number of T's = 31,005,462 bp (32.87%) number of G's = 22,973,736 bp (24.36%) number of N's = 12,767 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 474,043 number of insertions = 6,991 mapped reads with insertion percentage = 0.43% number of deletions = 17,238 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.2759X There is a 2.73% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 7595135 0.03047187994769329 0.4404335616698278 chr2 243199373 7969846 0.03277083284256658 0.4028701639447564 chr3 198022430 6235757 0.03149015492840887 0.19396400344232742 chr4 191154276 6129546 0.03206596330599479 0.22492300442735483 chr5 180915260 5660823 0.03128991440523038 0.19470358595744888 chr6 171115067 5327236 0.031132477656102605 0.21942620633658388 chr7 159138663 5227411 0.03284815205466443 0.3211432863523904 chr8 146364022 4768260 0.03257808807686359 0.2915231779193252 chr9 141213431 3989034 0.028248262022611718 0.23393929958486503 chr10 135534747 4590542 0.03386985331517976 0.3015540108709868 chr11 135006516 4325367 0.03203820917799256 0.24425756836375398 chr12 133851895 4257171 0.0318050857628874 0.19856463847955227 chr13 115169878 2953773 0.025647096717424673 0.17546715308815014 chr14 107349540 2869008 0.02672585276098994 0.18399451068683523 chr15 102531392 2755111 0.026870902133075497 0.18148828174417755 chr16 90354753 2731634 0.03023232214469116 0.2062080323431204 chr17 81195210 2641277 0.032529960819117285 0.20888799286051435 chr18 78077248 2495293 0.03195928473298649 0.4130345386411204 chr19 59128983 1997303 0.03377874772512154 0.34939822839300916 chr20 63025520 2041192 0.0323867538102026 0.20132498480735098 chr21 48129895 1235183 0.02566352991212634 0.19568296303054236 chr22 51304566 1133430 0.022092185713061093 0.16175104125254114 chrMT 16571 13439 0.8109951119425503 1.0170800920581218 chrX 155270560 5095269 0.03281542231830683 0.21662745287248164 chrY 59373566 310110 0.00522303140761328 0.17656605473869214