BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472725.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,454,108 number of mapped reads = 18,266,258 (98.98%) number of supplementary alignments = 83,923 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,173,015 number of mapped paired reads (second in pair) = 9,093,243 number of mapped paired reads (both in pair) = 18,146,528 number of mapped paired reads (singletons) = 119,730 number of mapped bases = 1,799,819,511 bp number of sequenced bases = 1,799,533,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,358,811 duplication rate = 44.93% >>>>>>> Insert size mean insert size = 27,408.6825 std insert size = 1,538,043.8232 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 55.0116 >>>>>>> ACTG content number of A's = 501,321,964 bp (27.86%) number of C's = 401,097,204 bp (22.29%) number of T's = 497,642,320 bp (27.65%) number of G's = 399,125,209 bp (22.18%) number of N's = 346,368 bp (0.02%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 12,005,593 number of insertions = 118,841 mapped reads with insertion percentage = 0.64% number of deletions = 114,885 mapped reads with deletion percentage = 0.62% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.5814X std coverageData = 26.615X There is a 4.9% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133321307 0.5348885650319002 22.61608880638132 chr2 243199373 120529125 0.49559800879914273 31.39061134759478 chr3 198022430 206476228 1.0426911133248895 36.18418312958416 chr4 191154276 80437923 0.42080106541796636 22.595487628460475 chr5 180915260 65029851 0.3594492305403093 13.024730001722975 chr6 171115067 121915469 0.7124765290247643 27.62317581010137 chr7 159138663 57959141 0.3642052780096563 12.28730972345753 chr8 146364022 115594734 0.7897756048272574 38.82575930904489 chr9 141213431 126656580 0.8969159597857232 29.59987835230697 chr10 135534747 63781284 0.4705899071033054 24.475284622900116 chr11 135006516 85870727 0.6360487593058101 28.106962704126648 chr12 133851895 98720177 0.7375329053055244 30.972868782208497 chr13 115169878 38305527 0.3326002220823747 16.800945079230235 chr14 107349540 80719473 0.7519312425558601 42.46084468916723 chr15 102531392 33126648 0.3230878597649391 15.025037223481371 chr16 90354753 78316475 0.8667665219559617 29.117491637044814 chr17 81195210 86903912 1.070308359323167 42.35056829545694 chr18 78077248 29508913 0.37794509611814187 16.83976047268886 chr19 59128983 25532810 0.43181547702249506 14.847269560439988 chr20 63025520 49097583 0.7790111529424906 29.35509893919186 chr21 48129895 6787788 0.14103060062773876 7.055357192798605 chr22 51304566 27703287 0.5399770266061699 21.621569055963892 chrMT 16571 2946 0.1777804598394786 0.5063270414636366 chrX 155270560 63508042 0.4090153471462974 14.876396338583143 chrY 59373566 4013561 0.06759844945139391 4.3630567183712925