BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038427.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,920,932 number of mapped reads = 14,975,180 (94.06%) number of supplementary alignments = 219,319 (1.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,573,222 number of mapped paired reads (second in pair) = 7,401,958 number of mapped paired reads (both in pair) = 14,779,184 number of mapped paired reads (singletons) = 195,996 number of mapped bases = 2,159,393,008 bp number of sequenced bases = 2,157,942,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,389,605 duplication rate = 9.74% >>>>>>> Insert size mean insert size = 66,692.9861 std insert size = 2,451,981.4825 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 53.7827 >>>>>>> ACTG content number of A's = 633,833,546 bp (29.37%) number of C's = 441,769,956 bp (20.47%) number of T's = 631,727,600 bp (29.27%) number of G's = 450,564,286 bp (20.88%) number of N's = 47,043 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 30,948,562 number of insertions = 369,938 mapped reads with insertion percentage = 2.33% number of deletions = 733,564 mapped reads with deletion percentage = 4.72% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.6975X std coverageData = 11.406X There is a 27% of reference with a coverageData >= 1X There is a 15.33% of reference with a coverageData >= 2X There is a 8.31% of reference with a coverageData >= 3X There is a 5.06% of reference with a coverageData >= 4X There is a 3.02% of reference with a coverageData >= 5X There is a 1.9% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.52% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% 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 128137213 0.5140898445344295 11.694619580508347 chr2 243199373 246859690 1.0150506843617562 17.194062231922278 chr3 198022430 141180699 0.7129530679933581 1.5839079535053688 chr4 191154276 133195102 0.6967937353386748 8.666743792235259 chr5 180915260 124289132 0.6870019256529273 1.671363657944268 chr6 171115067 146522756 0.8562820245396625 18.468422870432402 chr7 159138663 152455737 0.958005641909911 12.362872148205518 chr8 146364022 96324598 0.6581166374343006 3.5179772696938993 chr9 141213431 87068549 0.6165741345099107 19.726129052373878 chr10 135534747 90643109 0.6687813347229696 22.57864374776327 chr11 135006516 92295265 0.683635632816419 6.46790807500926 chr12 133851895 73079324 0.5459715306981646 1.3946865284995134 chr13 115169878 144634068 1.2558324321573042 2.358811678724915 chr14 107349540 39270972 0.36582338405921444 1.3208193374569097 chr15 102531392 46982420 0.45822473569850686 1.2004451873178166 chr16 90354753 75510693 0.8357135678296858 16.470062720846148 chr17 81195210 44907582 0.5530816657780675 6.369884324655019 chr18 78077248 35727809 0.45759564937534686 15.823503056819204 chr19 59128983 23429386 0.39624199185025727 6.836555436396711 chr20 63025520 65133145 1.03344081889368 3.1997491228583153 chr21 48129895 18825865 0.3911470199550612 4.361632073309949 chr22 51304566 11228405 0.21885781082330957 0.8753445710166214 chrMT 16571 1332940 80.43811477883048 48.81636118860881 chrX 155270560 109524047 0.7053754877936937 2.2785480183881597 chrY 59373566 30834502 0.5193304710719245 14.885715543876985