BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124911.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,918,832 number of mapped reads = 5,703,645 (96.36%) number of supplementary alignments = 5,654 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,905,433 number of mapped paired reads (second in pair) = 2,798,212 number of mapped paired reads (both in pair) = 5,579,518 number of mapped paired reads (singletons) = 124,127 number of mapped bases = 356,324,481 bp number of sequenced bases = 356,170,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 424,648 duplication rate = 5.55% >>>>>>> Insert size mean insert size = 26,614.423 std insert size = 1,583,166.2181 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 51.9736 >>>>>>> ACTG content number of A's = 96,742,481 bp (27.16%) number of C's = 64,812,301 bp (18.2%) number of T's = 105,878,002 bp (29.73%) number of G's = 88,735,121 bp (24.91%) number of N's = 3,092 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 2,422,796 number of insertions = 38,504 mapped reads with insertion percentage = 0.67% number of deletions = 103,955 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.1151X std coverageData = 0.7799X There is a 8.42% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 30817583 0.12364094771904299 0.9830598287206057 chr2 243199373 30277925 0.1244983678473546 0.9206852500726952 chr3 198022430 21471737 0.10843083281020235 0.4142631939387113 chr4 191154276 16464074 0.08612977090818517 0.4376192441843951 chr5 180915260 18250653 0.1008795664887528 0.4024171487766036 chr6 171115067 20641306 0.1206282203074496 0.6770957601371005 chr7 159138663 18407555 0.11566991108879682 0.9899332775921397 chr8 146364022 24298061 0.16601115949109407 0.6226324565275879 chr9 141213431 14657584 0.10379737887680103 0.6895984667671821 chr10 135534747 16119252 0.1189307713098841 1.4613323258011253 chr11 135006516 23702244 0.17556370390300272 0.7145893708584318 chr12 133851895 11740442 0.08771218367883399 0.3713387509394606 chr13 115169878 18398303 0.15974926186862853 0.7214311551727323 chr14 107349540 6165005 0.05742926332055079 0.3374579480505385 chr15 102531392 7920172 0.07724631301211633 0.3608496807242902 chr16 90354753 10672798 0.11812104671460946 1.333642630102603 chr17 81195210 9173942 0.1129862463561582 1.0077845878846836 chr18 78077248 9512321 0.12183217574471887 1.0586440721422505 chr19 59128983 7089818 0.11990427773804262 0.878709173670193 chr20 63025520 7144946 0.1133659190753206 0.4544087974576662 chr21 48129895 3095607 0.06431775926375904 0.3450483832739541 chr22 51304566 3190966 0.062196530421873175 0.3117276306882952 chrMT 16571 364399 21.990163538712206 16.156189621796052 chrX 155270560 26072422 0.16791606857088684 0.7473129441260576 chrY 59373566 675366 0.011374859983986813 0.46861209606362747