BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714248.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 357,840 number of mapped reads = 56,261 (15.72%) number of supplementary alignments = 1,882 (0.53%) number of secondary alignments = 0 number of mapped bases = 5,614,481 bp number of sequenced bases = 5,604,118 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,528 duplication rate = 32.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 11.7283 >>>>>>> ACTG content number of A's = 163,780 bp (2.92%) number of C's = 60,991 bp (1.09%) number of T's = 82,140 bp (1.47%) number of G's = 5,297,050 bp (94.52%) number of N's = 157 bp (0%) GC percentage = 95.61% >>>>>>> Mismatches and indels general error rate = 0.0319 number of mismatches = 133,183 number of insertions = 6,399 mapped reads with insertion percentage = 7.28% number of deletions = 2,573 mapped reads with deletion percentage = 4.34% homopolymer indels = 66.04% >>>>>>> Coverage mean coverageData = 0.0018X std coverageData = 6.7848X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 53513 2.146955533563144E-4 0.3371824724562496 chr2 243199373 5303717 0.0218081030990158 24.202376913078474 chr3 198022430 10002 5.0509429664104216E-5 0.017422802916348675 chr4 191154276 6099 3.19061656774029E-5 0.010830128962615333 chr5 180915260 9519 5.261579371469272E-5 0.016189606964266825 chr6 171115067 5298 3.096162186582903E-5 0.011824681125009279 chr7 159138663 12180 7.653702607769175E-5 0.07366935002837628 chr8 146364022 10195 6.96550959770701E-5 0.024454542489657886 chr9 141213431 5679 4.021572140683984E-5 0.014319803849265254 chr10 135534747 29963 2.2107246048129635E-4 0.337720613463267 chr11 135006516 6202 4.593852344134264E-5 0.02709830279322325 chr12 133851895 10968 8.194131282190664E-5 0.0685606975643391 chr13 115169878 4135 3.590348511092458E-5 0.012542840326690846 chr14 107349540 12337 1.1492364103283536E-4 0.07493771193784138 chr15 102531392 3881 3.785182200588869E-5 0.015567084397581936 chr16 90354753 4754 5.2614830345449565E-5 0.012025184802832007 chr17 81195210 11653 1.435183183835598E-4 0.10799238381872489 chr18 78077248 7539 9.655821885525474E-5 0.11157868042240093 chr19 59128983 3159 5.342557642163404E-5 0.015572440433526335 chr20 63025520 5170 8.203026329651862E-5 0.028472456010713243 chr21 48129895 483 1.0035342898628804E-5 0.0037170789265936724 chr22 51304566 3043 5.931245963565894E-5 0.013633302964739311 chrMT 16571 35271 2.128477460623982 9.019146060790064 chrX 155270560 55514 3.575307514830886E-4 0.056726254233125044 chrY 59373566 4207 7.085644813720638E-5 0.0200828946634258