BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472597.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 = 10,134,244 number of mapped reads = 9,385,006 (92.61%) number of supplementary alignments = 258,537 (2.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,738,883 number of mapped paired reads (second in pair) = 4,646,123 number of mapped paired reads (both in pair) = 9,170,264 number of mapped paired reads (singletons) = 214,742 number of mapped bases = 765,493,321 bp number of sequenced bases = 765,152,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,368,210 duplication rate = 12.88% >>>>>>> Insert size mean insert size = 203,771.652 std insert size = 4,346,017.5071 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 50.6358 >>>>>>> ACTG content number of A's = 199,093,325 bp (26.02%) number of C's = 153,024,402 bp (20%) number of T's = 227,282,873 bp (29.7%) number of G's = 185,266,517 bp (24.21%) number of N's = 485,413 bp (0.06%) GC percentage = 44.21% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 8,847,800 number of insertions = 72,820 mapped reads with insertion percentage = 0.76% number of deletions = 179,743 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.2473X std coverageData = 1.9726X There is a 13.81% of reference with a coverageData >= 1X There is a 6.19% of reference with a coverageData >= 2X There is a 2.1% of reference with a coverageData >= 3X There is a 0.97% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% 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 0.01% 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% 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 46826064 0.1878673915119353 2.533626435037025 chr2 243199373 71921659 0.2957312681887547 3.061072133130245 chr3 198022430 37810448 0.19094022833675964 0.6368526779076887 chr4 191154276 37001740 0.19357003554552973 1.1979010414987805 chr5 180915260 34056439 0.188245253606578 0.6672223081025266 chr6 171115067 46354416 0.2708961683660504 1.176256062163745 chr7 159138663 65197928 0.4096925710630106 3.5613136898866915 chr8 146364022 35180006 0.24035965614555194 1.772193788584219 chr9 141213431 25306053 0.17920429254353293 2.328783550153973 chr10 135534747 40488024 0.2987280007244194 2.13309753611561 chr11 135006516 32939013 0.24398091274350048 1.7671829499064629 chr12 133851895 37892710 0.28309431106672045 0.8233945859854614 chr13 115169878 32774230 0.28457293321088695 0.8240781200492191 chr14 107349540 18295183 0.17042628221788375 2.9305664243336573 chr15 102531392 23327078 0.22751157031009586 0.7275327233180134 chr16 90354753 26834748 0.296993208536578 1.336100315971765 chr17 81195210 23391666 0.288091699005397 1.5967122392187614 chr18 78077248 15749604 0.20171822654405033 3.561628714899635 chr19 59128983 16221523 0.27434131583152715 1.8197341862643373 chr20 63025520 28658955 0.4547198499909243 1.2680197157153157 chr21 48129895 11189225 0.23247973011368506 1.023377636685412 chr22 51304566 7609626 0.1483225878959779 0.5722288547527976 chrMT 16571 755494 45.59133425864462 25.77827919451439 chrX 155270560 47683866 0.30710178413731487 1.179385214962439 chrY 59373566 2027623 0.03415026478281598 1.0641859069202515