BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365332.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 96,559,960 number of mapped reads = 94,152,541 (97.51%) number of supplementary alignments = 782,373 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 47,356,125 number of mapped paired reads (second in pair) = 46,796,416 number of mapped paired reads (both in pair) = 93,446,546 number of mapped paired reads (singletons) = 705,995 number of mapped bases = 12,361,564,505 bp number of sequenced bases = 12,357,023,354 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,715,049 duplication rate = 30.8% >>>>>>> Insert size mean insert size = 97,127.1607 std insert size = 3,082,814.4017 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.1936 >>>>>>> ACTG content number of A's = 3,654,944,973 bp (29.58%) number of C's = 2,485,233,223 bp (20.11%) number of T's = 3,604,091,279 bp (29.17%) number of G's = 2,612,030,270 bp (21.14%) number of N's = 723,609 bp (0.01%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 92,132,270 number of insertions = 3,631,631 mapped reads with insertion percentage = 3.74% number of deletions = 1,873,302 mapped reads with deletion percentage = 1.93% homopolymer indels = 50.28% >>>>>>> Coverage mean coverageData = 3.9931X std coverageData = 38.484X There is a 67.48% of reference with a coverageData >= 1X There is a 58.82% of reference with a coverageData >= 2X There is a 48.46% of reference with a coverageData >= 3X There is a 40.85% of reference with a coverageData >= 4X There is a 33.22% of reference with a coverageData >= 5X There is a 27.4% of reference with a coverageData >= 6X There is a 22.05% of reference with a coverageData >= 7X There is a 17.92% of reference with a coverageData >= 8X There is a 14.3% of reference with a coverageData >= 9X There is a 11.5% of reference with a coverageData >= 10X There is a 9.12% of reference with a coverageData >= 11X There is a 7.27% of reference with a coverageData >= 12X There is a 5.74% of reference with a coverageData >= 13X There is a 4.56% of reference with a coverageData >= 14X There is a 3.59% of reference with a coverageData >= 15X There is a 2.84% of reference with a coverageData >= 16X There is a 2.24% of reference with a coverageData >= 17X There is a 1.77% of reference with a coverageData >= 18X There is a 1.4% of reference with a coverageData >= 19X There is a 1.11% of reference with a coverageData >= 20X There is a 0.88% of reference with a coverageData >= 21X There is a 0.7% of reference with a coverageData >= 22X There is a 0.56% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1087339889 4.362436027792284 105.91310794504948 chr2 243199373 1088512249 4.475802036710021 25.22556346688082 chr3 198022430 846134517 4.272922602757678 5.522705881053411 chr4 191154276 806398361 4.218573488777201 16.240613963858504 chr5 180915260 761579934 4.209594779345866 5.4633705077447585 chr6 171115067 740297370 4.326313181994664 21.544078312283332 chr7 159138663 666181399 4.186169384871607 24.216167583770908 chr8 146364022 616661369 4.213203221485673 13.98678208206541 chr9 141213431 534387557 3.7842544665599123 37.570580033585365 chr10 135534747 636624775 4.697133311504245 63.39268695646599 chr11 135006516 589925006 4.369603953041793 27.44967073828552 chr12 133851895 581305053 4.34289744646499 24.04308872946343 chr13 115169878 391826215 3.402158809267819 4.510865882547732 chr14 107349540 382817375 3.5660830498202416 4.954434764007113 chr15 102531392 369468689 3.6034689649000375 11.845204912157625 chr16 90354753 351003674 3.8847283883339263 12.154720947922705 chr17 81195210 378853812 4.66596258572396 24.22864220649722 chr18 78077248 319408567 4.090930138828663 38.13965849329342 chr19 59128983 236455466 3.998977388127917 53.782871328595725 chr20 63025520 261190615 4.14420404623397 7.591784069310863 chr21 48129895 163882085 3.4049956892696316 12.12627637646832 chr22 51304566 159292603 3.1048426177116477 10.577147962094376 chrMT 16571 7939867 479.1422967835375 109.07180226502764 chrX 155270560 297403909 1.9153914882512177 8.853871481805355 chrY 59373566 86674149 1.4598103977787018 28.62856298027892