BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926887.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 35,763,590 number of mapped reads = 31,457,295 (87.96%) number of supplementary alignments = 232,248 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,769,232 number of mapped paired reads (second in pair) = 15,688,063 number of mapped paired reads (both in pair) = 31,182,644 number of mapped paired reads (singletons) = 274,651 number of mapped bases = 2,978,449,718 bp number of sequenced bases = 2,976,191,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,372,555 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 61,824.917 std insert size = 2,461,294.7505 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.5467 >>>>>>> ACTG content number of A's = 844,841,537 bp (28.39%) number of C's = 607,930,059 bp (20.43%) number of T's = 848,992,322 bp (28.53%) number of G's = 674,220,762 bp (22.65%) number of N's = 206,431 bp (0.01%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 27,355,050 number of insertions = 464,336 mapped reads with insertion percentage = 1.45% number of deletions = 1,605,903 mapped reads with deletion percentage = 4.97% homopolymer indels = 53.14% >>>>>>> Coverage mean coverageData = 0.9621X std coverageData = 3.5834X There is a 32.91% of reference with a coverageData >= 1X There is a 20.07% of reference with a coverageData >= 2X There is a 12.49% of reference with a coverageData >= 3X There is a 8.33% of reference with a coverageData >= 4X There is a 5.71% of reference with a coverageData >= 5X There is a 4.02% of reference with a coverageData >= 6X There is a 2.88% of reference with a coverageData >= 7X There is a 2.1% of reference with a coverageData >= 8X There is a 1.55% of reference with a coverageData >= 9X There is a 1.15% of reference with a coverageData >= 10X There is a 0.86% of reference with a coverageData >= 11X There is a 0.65% of reference with a coverageData >= 12X There is a 0.5% of reference with a coverageData >= 13X There is a 0.38% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 242621943 0.9734055707728808 3.3615589292723933 chr2 243199373 260573808 1.071441117572289 5.423099883648744 chr3 198022430 198515424 1.0024895866594508 2.1746517909291136 chr4 191154276 170585611 0.8923975679204791 2.3812668240125454 chr5 180915260 182774924 1.0102791992228848 2.126659839375306 chr6 171115067 167102256 0.976549049301427 2.1052199414934205 chr7 159138663 149340870 0.9384323531736596 2.3074388789746014 chr8 146364022 148655495 1.0156559854579563 2.4329596320538127 chr9 141213431 129623624 0.9179270206953615 3.6631709873962017 chr10 135534747 153150029 1.1299687525885889 9.645822789388271 chr11 135006516 147297904 1.0910429241800448 2.6838804804123537 chr12 133851895 131875656 0.9852356292751776 2.3090367344875666 chr13 115169878 89217568 0.7746606104766387 1.9349359367287575 chr14 107349540 89068175 0.8297024374766767 2.02037426359504 chr15 102531392 84788604 0.8269526273475347 2.08093630364576 chr16 90354753 97019512 1.0737621295915667 5.256968460257211 chr17 81195210 82290911 1.013494650731244 2.5856033070234217 chr18 78077248 79335269 1.0161125171829828 3.8429445912262894 chr19 59128983 50726003 0.857887290231256 2.504353550270474 chr20 63025520 74650454 1.184448045807476 2.535287089967665 chr21 48129895 37471871 0.778557090141169 3.536014702571034 chr22 51304566 41200770 0.8030624408751454 2.1379673695048775 chrMT 16571 384487 23.20240178625309 15.869671386894595 chrX 155270560 165579718 1.066394801435636 2.312882347029208 chrY 59373566 4598832 0.07745588331345973 2.024896333534278