BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714113.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 = 634,126 number of mapped reads = 453,510 (71.52%) number of supplementary alignments = 15,749 (2.48%) number of secondary alignments = 0 number of mapped bases = 58,506,107 bp number of sequenced bases = 57,107,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 397,955 duplication rate = 43.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9452 >>>>>>> ACTG content number of A's = 15,704,752 bp (27.5%) number of C's = 11,534,098 bp (20.2%) number of T's = 14,838,489 bp (25.98%) number of G's = 15,029,878 bp (26.32%) number of N's = 562 bp (0%) GC percentage = 46.52% >>>>>>> Mismatches and indels general error rate = 0.047 number of mismatches = 2,508,038 number of insertions = 62,671 mapped reads with insertion percentage = 13.17% number of deletions = 222,374 mapped reads with deletion percentage = 45.38% homopolymer indels = 31.36% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 4.9786X 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 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 4239829 0.017010304660384376 3.54862032027191 chr2 243199373 7675118 0.03155895471819329 13.451346326971299 chr3 198022430 3595903 0.01815906915191375 4.2260534800155565 chr4 191154276 2361708 0.012354983887464803 2.6330144674549945 chr5 180915260 2901677 0.016038873669363216 2.2136984202214607 chr6 171115067 1882971 0.011004121571597199 1.4006677698673982 chr7 159138663 3088649 0.019408539331513677 3.1964724980449355 chr8 146364022 3202355 0.02187938645195197 5.236368652457187 chr9 141213431 2328719 0.016490775583520804 3.4638587436098085 chr10 135534747 2342103 0.017280461666409428 2.2520391614731627 chr11 135006516 2852559 0.02112904683800595 5.6904696744598064 chr12 133851895 3560377 0.02659937687098117 4.364930857774195 chr13 115169878 1310999 0.011383176076647402 1.853062976278915 chr14 107349540 1637371 0.01525270625286331 3.358670630423386 chr15 102531392 1620339 0.01580334537933514 2.509855716199971 chr16 90354753 1523806 0.01686470218119018 2.601952278409223 chr17 81195210 1715810 0.021131911599218723 3.8042720383625257 chr18 78077248 1289460 0.016515182502334098 2.1783082179337443 chr19 59128983 1404590 0.023754678818000304 3.7232754144256255 chr20 63025520 1309536 0.020777869028292033 3.661335735249577 chr21 48129895 392068 0.008146038963932916 0.9362332326610525 chr22 51304566 501884 0.009782443145508725 1.921998452435801 chrMT 16571 340563 20.551747027940376 163.04797383615838 chrX 155270560 5115759 0.0329473855185426 3.344701514147065 chrY 59373566 311954 0.005254088999808434 1.0907724304255213