BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617366.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,139,374 (94.19%) number of supplementary alignments = 95,816 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,180,843 number of mapped paired reads (second in pair) = 14,958,531 number of mapped paired reads (both in pair) = 29,538,672 number of mapped paired reads (singletons) = 600,702 number of mapped bases = 2,951,707,414 bp number of sequenced bases = 2,950,835,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,603,034 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 64,337.2935 std insert size = 2,425,571.6239 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.3893 >>>>>>> ACTG content number of A's = 894,444,981 bp (30.31%) number of C's = 585,434,672 bp (19.84%) number of T's = 882,588,423 bp (29.91%) number of G's = 587,220,201 bp (19.9%) number of N's = 1,146,775 bp (0.04%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 30,994,228 number of insertions = 300,979 mapped reads with insertion percentage = 0.97% number of deletions = 362,218 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.9535X std coverageData = 9.7907X There is a 52.86% of reference with a coverageData >= 1X There is a 23.81% of reference with a coverageData >= 2X There is a 9.13% of reference with a coverageData >= 3X There is a 3.21% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 191632236 0.7688335348219654 19.843487927725075 chr2 243199373 291614469 1.1990757435053092 8.903958224309873 chr3 198022430 234785097 1.1856490045092367 1.4718991292794643 chr4 191154276 161522752 0.8449863397248828 9.341991102218628 chr5 180915260 185207850 1.0237270753169192 1.4755628014479392 chr6 171115067 138251193 0.8079428388383824 3.612488209095712 chr7 159138663 239641504 1.5058660132138977 10.844376929989785 chr8 146364022 124196497 0.848545259298764 7.718853690301226 chr9 141213431 124197634 0.8795029843868039 14.989788220172935 chr10 135534747 124254216 0.916770191779677 20.167472377495912 chr11 135006516 158288936 1.1724540465883884 5.54251311521831 chr12 133851895 130028099 0.9714326345547816 1.4540783801474808 chr13 115169878 128501197 1.1157535219408672 1.3296483708910265 chr14 107349540 85294891 0.7945529249589705 1.3917747498437918 chr15 102531392 66480005 0.6483868374672997 1.1443815355154845 chr16 90354753 74152089 0.8206772365367431 7.8963447485004234 chr17 81195210 92092534 1.1342114146881324 7.091629828816149 chr18 78077248 53411536 0.6840857915483907 15.274061999903367 chr19 59128983 54903038 0.9285300577552636 9.52415084876134 chr20 63025520 84828086 1.3459323461353432 2.508287232727266 chr21 48129895 47089165 0.9783766409629607 3.234822465454514 chr22 51304566 26208726 0.5108458767588054 0.9289453188492829 chrMT 16571 2000560 120.7265705147547 19.71887973624669 chrX 155270560 122925360 0.7916849143842851 2.9911324211985657 chrY 59373566 10199744 0.17178931108837223 8.469784680785319