BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472435.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,539,316 number of mapped reads = 15,373,067 (98.93%) number of supplementary alignments = 60,525 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,714,040 number of mapped paired reads (second in pair) = 7,659,027 number of mapped paired reads (both in pair) = 15,282,146 number of mapped paired reads (singletons) = 90,921 number of mapped bases = 1,506,165,856 bp number of sequenced bases = 1,505,996,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,400,973 duplication rate = 46.5% >>>>>>> Insert size mean insert size = 18,031.3304 std insert size = 1,335,342.9901 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.7611 >>>>>>> ACTG content number of A's = 414,595,773 bp (27.53%) number of C's = 339,473,521 bp (22.54%) number of T's = 415,324,881 bp (27.58%) number of G's = 336,414,990 bp (22.34%) number of N's = 187,746 bp (0.01%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 8,423,059 number of insertions = 97,299 mapped reads with insertion percentage = 0.63% number of deletions = 72,805 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.4865X std coverageData = 15.9014X There is a 4.24% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 131612127 0.528031290240998 15.864262900594616 chr2 243199373 130754170 0.5376418877527287 18.95620950972324 chr3 198022430 122060814 0.6163989301615984 19.842750991948122 chr4 191154276 50950013 0.2665387040570309 12.777846957371526 chr5 180915260 60069443 0.33203082481820495 9.519845574807617 chr6 171115067 120124050 0.7020074392397018 14.800949969689393 chr7 159138663 105946578 0.6657500823668476 21.269328830032702 chr8 146364022 136342596 0.9315308102150951 23.21538380449753 chr9 141213431 48852772 0.34594989764111034 8.603517416808995 chr10 135534747 36424854 0.2687491938875276 11.628323799378206 chr11 135006516 39849245 0.2951653459452283 8.704739354115304 chr12 133851895 48271468 0.3606334299562961 9.559010443390203 chr13 115169878 44520206 0.38656119788544013 11.701914269403535 chr14 107349540 22326337 0.20797794755338495 6.000875287760449 chr15 102531392 29274717 0.2855195509293388 9.952711612582208 chr16 90354753 63293427 0.70049914252989 19.31810821301763 chr17 81195210 50310086 0.6196188913114455 12.481817758224597 chr18 78077248 10394802 0.13313484102308523 4.4721124173395115 chr19 59128983 33448784 0.5656918536887401 10.996567127093051 chr20 63025520 97133450 1.5411764948547826 41.93918360684842 chr21 48129895 10436291 0.21683593949249214 12.10561040670522 chr22 51304566 13602770 0.26513760977921536 8.744060224276893 chrMT 16571 4860 0.2932834469856979 0.7227531785153901 chrX 155270560 99811286 0.6428217042561063 19.741109789639587 chrY 59373566 350710 0.005906837396291811 0.8623981051736347