BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,673,672 number of mapped reads = 2,477,594 (92.67%) number of supplementary alignments = 16,225 (0.61%) number of secondary alignments = 0 number of mapped bases = 169,657,124 bp number of sequenced bases = 169,595,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,071 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0585 >>>>>>> ACTG content number of A's = 48,349,671 bp (28.51%) number of C's = 31,293,375 bp (18.45%) number of T's = 53,890,640 bp (31.78%) number of G's = 36,039,423 bp (21.25%) number of N's = 22,212 bp (0.01%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,250,484 number of insertions = 12,150 mapped reads with insertion percentage = 0.49% number of deletions = 34,680 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.4533X There is a 4.61% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12932407 0.051885154581019076 0.7756126314989176 chr2 243199373 14463295 0.059470938685355905 0.45156866151797864 chr3 198022430 11976928 0.06048268370406322 0.2841841221891493 chr4 191154276 11418930 0.05973672281335731 0.29313463496933656 chr5 180915260 10140812 0.05605282826888124 0.2722525778121602 chr6 171115067 10692872 0.062489365708514724 0.33806862931123066 chr7 159138663 9590168 0.06026296702015148 0.5776764953988832 chr8 146364022 9084435 0.06206740478886266 0.9164567423447049 chr9 141213431 6708857 0.04750863251810658 0.3691321062804459 chr10 135534747 8420435 0.06212750004247988 0.4721829876534853 chr11 135006516 8076112 0.05982016453191045 0.3576537573072256 chr12 133851895 7088750 0.05295965365301702 0.265922492343372 chr13 115169878 6192490 0.053768312579092946 0.26601120617827345 chr14 107349540 4902638 0.04566985568824981 0.25542509364920335 chr15 102531392 4481058 0.043704254010323004 0.24057815682693587 chr16 90354753 4067002 0.045011489323644106 0.28062281703329023 chr17 81195210 4107955 0.05059356333951227 0.28663839334953545 chr18 78077248 4446494 0.056949932456635766 0.6856109547125343 chr19 59128983 2784191 0.04708673917154976 0.5597447558554492 chr20 63025520 3302571 0.052400535529099956 0.2690965553011209 chr21 48129895 2223836 0.046204879524461874 0.2659154408216984 chr22 51304566 1535893 0.029936770150243548 0.19581944257049055 chrMT 16571 77910 4.701587110011466 3.699716168221913 chrX 155270560 10518410 0.06774246193225554 0.3269624837292769 chrY 59373566 422675 0.007118908774992562 0.15230039643956506