BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524305.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 = 523,689 number of mapped reads = 479,331 (91.53%) number of supplementary alignments = 1,973 (0.38%) number of secondary alignments = 0 number of mapped bases = 27,762,566 bp number of sequenced bases = 27,754,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,203 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8007 >>>>>>> ACTG content number of A's = 6,752,189 bp (24.33%) number of C's = 5,198,313 bp (18.73%) number of T's = 8,910,701 bp (32.1%) number of G's = 6,889,649 bp (24.82%) number of N's = 4,099 bp (0.01%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 140,239 number of insertions = 1,851 mapped reads with insertion percentage = 0.38% number of deletions = 4,740 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.009X std coverageData = 0.1154X There is a 0.86% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2354422 0.009446002543760964 0.1750916364478449 chr2 243199373 1817273 0.007472358902833191 0.12825753770818127 chr3 198022430 1948192 0.00983823903181069 0.10230415995275091 chr4 191154276 1462304 0.007649862878296272 0.09244028797615901 chr5 180915260 1623282 0.008972609607392986 0.0973236952516496 chr6 171115067 1782629 0.01041772084278236 0.10674764776194137 chr7 159138663 1267207 0.007962910936357433 0.12878240076602754 chr8 146364022 2873502 0.01963257063269278 0.15756443540324358 chr9 141213431 1133426 0.008026332849316578 0.10033252546309447 chr10 135534747 1407437 0.010384326020839512 0.11917188709543754 chr11 135006516 1340482 0.00992901705573974 0.108919663489937 chr12 133851895 1107496 0.008274040498268628 0.09386127320872253 chr13 115169878 705618 0.006126758248367685 0.08078448637628761 chr14 107349540 588553 0.005482585207165303 0.07957472531456353 chr15 102531392 843392 0.008225695404583993 0.09358872802846185 chr16 90354753 849197 0.009398476248393928 0.10105315098177815 chr17 81195210 858709 0.010575857861565972 0.10955455609365657 chr18 78077248 652559 0.008357863740279371 0.13780495029033538 chr19 59128983 487560 0.008245702450184201 0.13570855846771115 chr20 63025520 623283 0.00988937497064681 0.10226949167316678 chr21 48129895 393240 0.008170389733864991 0.09486289535715194 chr22 51304566 196135 0.003822954081708829 0.06323531725358178 chrMT 16571 11908 0.7186047915032285 0.9762037611239206 chrX 155270560 1359942 0.008758530915326124 0.0998371610029371 chrY 59373566 74818 0.0012601230655406481 0.0468547609309522