BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124814.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 = 27,141,418 number of mapped reads = 26,751,296 (98.56%) number of supplementary alignments = 126,120 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,416,682 number of mapped paired reads (second in pair) = 13,334,614 number of mapped paired reads (both in pair) = 26,579,542 number of mapped paired reads (singletons) = 171,754 number of mapped bases = 2,318,236,138 bp number of sequenced bases = 2,316,931,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,426,683 duplication rate = 12.16% >>>>>>> Insert size mean insert size = 33,875.5932 std insert size = 1,723,665.1824 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.4666 >>>>>>> ACTG content number of A's = 654,544,762 bp (28.25%) number of C's = 427,276,536 bp (18.44%) number of T's = 698,926,215 bp (30.17%) number of G's = 536,162,753 bp (23.14%) number of N's = 21,713 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 18,909,676 number of insertions = 333,935 mapped reads with insertion percentage = 1.21% number of deletions = 773,411 mapped reads with deletion percentage = 2.83% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.7489X std coverageData = 9.1181X There is a 29.31% of reference with a coverageData >= 1X There is a 15.56% of reference with a coverageData >= 2X There is a 8.84% of reference with a coverageData >= 3X There is a 5.38% of reference with a coverageData >= 4X There is a 3.42% of reference with a coverageData >= 5X There is a 2.25% of reference with a coverageData >= 6X There is a 1.53% of reference with a coverageData >= 7X There is a 1.07% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.01% 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 182003375 0.7302022930566741 8.1602484872781 chr2 243199373 222006277 0.9128571108610547 9.534810985627901 chr3 198022430 191529937 0.9672133454780855 2.120627594812228 chr4 191154276 154151774 0.8064259781455269 4.8142257442141165 chr5 180915260 99605779 0.5505659334652035 2.429665664361654 chr6 171115067 147345803 0.8610919282753751 20.469700135486576 chr7 159138663 129184884 0.8117756022620348 8.75652041894846 chr8 146364022 150348009 1.0272197152384894 3.434952606825364 chr9 141213431 127909859 0.905791029183336 12.144139326077722 chr10 135534747 112788049 0.8321707274076366 16.503813187871444 chr11 135006516 91417268 0.677132265230813 10.276979486253511 chr12 133851895 97330679 0.7271520436823102 2.643573372493943 chr13 115169878 48632625 0.42226861610463806 1.169061807165133 chr14 107349540 49021078 0.4566491668245621 2.3444372884256137 chr15 102531392 86921637 0.8477563339820843 2.0398211678011795 chr16 90354753 81259079 0.8993337517064542 16.129735462884167 chr17 81195210 42656476 0.5253570500033191 7.202222759754589 chr18 78077248 47309740 0.6059350350053322 11.976283115008698 chr19 59128983 21482813 0.3633211990133502 6.169036372511754 chr20 63025520 61628590 0.9778354863236353 2.470103703581636 chr21 48129895 32473048 0.6746960075437521 4.031876973060743 chr22 51304566 33134191 0.6458331798382234 1.8239809846336341 chrMT 16571 624193 37.66779313258102 24.210444852304953 chrX 155270560 99270657 0.6393398529637556 4.417008819699548 chrY 59373566 8200318 0.1381139546174471 10.751959322219298