BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714104.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 = 569,368 number of mapped reads = 399,166 (70.11%) number of supplementary alignments = 14,647 (2.57%) number of secondary alignments = 0 number of mapped bases = 51,094,075 bp number of sequenced bases = 50,152,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,859 duplication rate = 42.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.395 >>>>>>> ACTG content number of A's = 13,784,552 bp (27.49%) number of C's = 10,788,980 bp (21.51%) number of T's = 13,079,141 bp (26.08%) number of G's = 12,499,034 bp (24.92%) number of N's = 351 bp (0%) GC percentage = 46.43% >>>>>>> Mismatches and indels general error rate = 0.0417 number of mismatches = 1,908,741 number of insertions = 58,106 mapped reads with insertion percentage = 14.1% number of deletions = 164,358 mapped reads with deletion percentage = 39.17% homopolymer indels = 28.25% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 2.2557X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4127380 0.016559156336063852 1.8243826310841968 chr2 243199373 5396438 0.0221893581937812 5.188761267138501 chr3 198022430 2620499 0.013233344323670808 1.3691258312608139 chr4 191154276 2376850 0.012434197391430575 1.4023200420449395 chr5 180915260 2888550 0.015966314837123192 1.597296548453585 chr6 171115067 1866302 0.010906707589928361 1.0313294727029947 chr7 159138663 1993860 0.01252907346594963 1.3301104895758709 chr8 146364022 2588150 0.017682965831589407 2.3975626247365045 chr9 141213431 2039163 0.014440290739766815 1.6853617046617277 chr10 135534747 2685116 0.019811273931104913 1.8085476098713282 chr11 135006516 2371348 0.017564692951560944 1.8081067439739553 chr12 133851895 2054108 0.01534612565627106 1.6121978367161416 chr13 115169878 1322725 0.011484990893191707 1.4519239121756147 chr14 107349540 1765592 0.01644713149213308 1.8620212644805625 chr15 102531392 1607867 0.01568170458467978 1.7800387835791742 chr16 90354753 1903558 0.021067602276550964 2.330402266219318 chr17 81195210 1899414 0.02339317799658379 2.4299075072920506 chr18 78077248 1175232 0.015052169871561046 1.4687482797947218 chr19 59128983 1199211 0.020281272214676852 2.172412988541862 chr20 63025520 1415558 0.02246007648965054 1.9922555306859093 chr21 48129895 497236 0.010331125800295222 1.156172648015748 chr22 51304566 626876 0.012218717530911381 1.341595782820706 chrMT 16571 456707 27.56061794701587 247.5543932011724 chrX 155270560 3955303 0.025473618437390835 1.60346295562678 chrY 59373566 261032 0.004396434601890006 0.7781513977235015