BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714246.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 = 348,510 number of mapped reads = 52,313 (15.01%) number of supplementary alignments = 1,231 (0.35%) number of secondary alignments = 0 number of mapped bases = 5,121,964 bp number of sequenced bases = 5,106,008 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,013 duplication rate = 26.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 18.897 >>>>>>> ACTG content number of A's = 226,743 bp (4.44%) number of C's = 111,031 bp (2.17%) number of T's = 146,461 bp (2.87%) number of G's = 4,621,597 bp (90.51%) number of N's = 176 bp (0%) GC percentage = 92.69% >>>>>>> Mismatches and indels general error rate = 0.0335 number of mismatches = 129,089 number of insertions = 5,935 mapped reads with insertion percentage = 7.57% number of deletions = 3,123 mapped reads with deletion percentage = 5.76% homopolymer indels = 61.35% >>>>>>> Coverage mean coverageData = 0.0017X std coverageData = 5.7905X 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 85554 3.4324488202579044E-4 0.7966435698754174 chr2 243199373 4573897 0.018807190757025513 20.62772198668719 chr3 198022430 8640 4.363142094559692E-5 0.010448569344927496 chr4 191154276 9234 4.8306531212516535E-5 0.009783197656942825 chr5 180915260 7701 4.256689015619799E-5 0.00947496936535379 chr6 171115067 15750 9.20433266113264E-5 0.02812041476525674 chr7 159138663 14329 9.004097263277875E-5 0.06496929268281391 chr8 146364022 6897 4.712223609159907E-5 0.012676744997533343 chr9 141213431 8261 5.850010116955518E-5 0.02725074533497061 chr10 135534747 76236 5.624830656894206E-4 1.0465094115748432 chr11 135006516 10583 7.838880902607693E-5 0.02914887170269223 chr12 133851895 15815 1.1815297796120108E-4 0.063160714977616 chr13 115169878 5482 4.759925160292347E-5 0.009781299938415288 chr14 107349540 10079 9.38895499691941E-5 0.052828284211614646 chr15 102531392 4718 4.601517552790076E-5 0.013553154306175517 chr16 90354753 4589 5.078869508945479E-5 0.010110776052556936 chr17 81195210 8731 1.0753097380990825E-4 0.08967535782485345 chr18 78077248 4244 5.4356424037896416E-5 0.016133522393484406 chr19 59128983 3088 5.222481164609241E-5 0.012152136757818854 chr20 63025520 4348 6.898792743003152E-5 0.023934461327364077 chr21 48129895 2008 4.172043176075909E-5 0.008061579368395378 chr22 51304566 1379 2.6878699256514517E-5 0.005381781941000825 chrMT 16571 13099 0.7904773399312052 5.573134506474104 chrX 155270560 222809 0.001434972605238237 0.22692128832610486 chrY 59373566 4493 7.567340657962165E-5 0.012585630867626768