BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525038.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 = 1,218,587 number of mapped reads = 1,119,696 (91.88%) number of supplementary alignments = 3,622 (0.3%) number of secondary alignments = 0 number of mapped bases = 64,991,507 bp number of sequenced bases = 64,971,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,104 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6098 >>>>>>> ACTG content number of A's = 16,074,954 bp (24.74%) number of C's = 11,471,151 bp (17.66%) number of T's = 21,512,796 bp (33.11%) number of G's = 15,911,438 bp (24.49%) number of N's = 701 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 319,349 number of insertions = 4,137 mapped reads with insertion percentage = 0.37% number of deletions = 12,227 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2008X There is a 1.93% of reference with a coverageData >= 1X There is a 0.12% 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 4908227 0.019691934889903444 0.3147743120767276 chr2 243199373 5633027 0.023162177313672597 0.23264374379955552 chr3 198022430 4226955 0.021345839458691625 0.15678776887699247 chr4 191154276 4218517 0.022068650978019452 0.17606521911558456 chr5 180915260 4516905 0.024966965196855147 0.16938897198339686 chr6 171115067 3498571 0.020445721474661258 0.17721739551626953 chr7 159138663 3600654 0.022625890730274642 0.23802923174788596 chr8 146364022 2980272 0.020362053182714532 0.21525539718153205 chr9 141213431 2741988 0.019417331485983087 0.17872443326065243 chr10 135534747 3063717 0.022604660928757996 0.22001908178593246 chr11 135006516 2939621 0.021773919415859898 0.18909777377480533 chr12 133851895 3016950 0.022539464233957987 0.16153717016123217 chr13 115169878 2063063 0.01791321685692851 0.14502047695848982 chr14 107349540 1970789 0.018358616161746014 0.14880885190559603 chr15 102531392 2025200 0.019751999465685594 0.15581479391040154 chr16 90354753 1855330 0.02053383954245329 0.15994864248006857 chr17 81195210 1804553 0.022224870161675795 0.17626378376336918 chr18 78077248 1567616 0.020077756838970555 0.2692016796258666 chr19 59128983 1330672 0.022504564301401905 0.2323966460968502 chr20 63025520 1411346 0.02239324641827628 0.16127286994922263 chr21 48129895 857253 0.017811237693329686 0.15705279341807302 chr22 51304566 804717 0.015685095162874977 0.13303609076540215 chrMT 16571 7368 0.4446321887635025 0.7597037857513932 chrX 155270560 3739944 0.024086626595537494 0.17702290558162884 chrY 59373566 208252 0.003507486816607916 0.11369559245908678