BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524840.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 = 860,964 number of mapped reads = 795,660 (92.42%) number of supplementary alignments = 4,126 (0.48%) number of secondary alignments = 0 number of mapped bases = 46,976,465 bp number of sequenced bases = 46,962,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,762 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1804 >>>>>>> ACTG content number of A's = 12,194,998 bp (25.97%) number of C's = 7,860,538 bp (16.74%) number of T's = 15,141,359 bp (32.24%) number of G's = 11,759,275 bp (25.04%) number of N's = 6,405 bp (0.01%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 222,042 number of insertions = 3,315 mapped reads with insertion percentage = 0.41% number of deletions = 8,844 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.54% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1795X There is a 1.43% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3946748 0.01583445603531716 0.34134749977365336 chr2 243199373 3006056 0.012360459498388592 0.16635469757680468 chr3 198022430 3442918 0.017386505154996835 0.13658114486543757 chr4 191154276 2573919 0.013465139539959859 0.1246071354576171 chr5 180915260 2886966 0.015957559356795 0.1313132529035145 chr6 171115067 3067186 0.01792469858893256 0.14884995049876673 chr7 159138663 2175733 0.013671932131288547 0.2287217100047244 chr8 146364022 5071111 0.03464725094805061 0.24472377864011652 chr9 141213431 1928879 0.013659316867671037 0.1537275784155243 chr10 135534747 2350333 0.017341184102405857 0.17775199346782627 chr11 135006516 2259262 0.01673446635716457 0.16368856365241616 chr12 133851895 1826148 0.013643049282193577 0.12242934299349688 chr13 115169878 1252738 0.010877305956684265 0.10807201577717188 chr14 107349540 953901 0.008885934676571507 0.10239581616203645 chr15 102531392 1391399 0.01357046825229877 0.12066631001054814 chr16 90354753 1317730 0.014583958853830301 0.13307777300651952 chr17 81195210 1236492 0.015228632329419433 0.13621709886580097 chr18 78077248 1158293 0.014835218065062949 0.24498704569053661 chr19 59128983 666939 0.011279392375140293 0.2202360488475793 chr20 63025520 977054 0.015502513902304971 0.1300649021939959 chr21 48129895 679545 0.014118979482502507 0.12782682551740893 chr22 51304566 285436 0.005563559391575401 0.07697862401466922 chrMT 16571 3167 0.19111701164685294 0.43598604191885754 chrX 155270560 2401390 0.015465842333537021 0.13950495770978374 chrY 59373566 117122 0.0019726286947292335 0.0612720582146243