BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038485.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 = 17,263,240 number of mapped reads = 16,341,672 (94.66%) number of supplementary alignments = 236,880 (1.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,291,373 number of mapped paired reads (second in pair) = 8,050,299 number of mapped paired reads (both in pair) = 16,054,406 number of mapped paired reads (singletons) = 287,266 number of mapped bases = 2,209,832,513 bp number of sequenced bases = 2,208,346,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,046,537 duplication rate = 13.23% >>>>>>> Insert size mean insert size = 79,645.4414 std insert size = 2,734,259.49 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.493 >>>>>>> ACTG content number of A's = 635,659,128 bp (28.78%) number of C's = 432,761,413 bp (19.6%) number of T's = 648,348,415 bp (29.36%) number of G's = 491,402,245 bp (22.25%) number of N's = 175,196 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 27,756,540 number of insertions = 386,487 mapped reads with insertion percentage = 2.26% number of deletions = 771,333 mapped reads with deletion percentage = 4.56% homopolymer indels = 48.34% >>>>>>> Coverage mean coverageData = 0.7138X std coverageData = 8.7355X There is a 27.88% of reference with a coverageData >= 1X There is a 15.76% of reference with a coverageData >= 2X There is a 8.92% of reference with a coverageData >= 3X There is a 5.43% of reference with a coverageData >= 4X There is a 3.32% of reference with a coverageData >= 5X There is a 2.1% of reference with a coverageData >= 6X There is a 1.35% of reference with a coverageData >= 7X There is a 0.89% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% 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 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 198894734 0.7979708664396868 12.479559157688723 chr2 243199373 193585044 0.7959931870383564 9.69220595993112 chr3 198022430 197796183 0.9988574678131159 2.027063139778069 chr4 191154276 94086944 0.4922042340292717 8.614517334039968 chr5 180915260 152272559 0.8416789108889985 1.7150448907939133 chr6 171115067 128697833 0.7521128048881868 7.6026196689231424 chr7 159138663 104493430 0.6566187501525007 8.134614590063974 chr8 146364022 138638398 0.9472163726137561 3.5350996909127193 chr9 141213431 92067959 0.6519773533439606 15.125307942133276 chr10 135534747 114701495 0.8462884798095355 21.51421791491553 chr11 135006516 98876868 0.7323858946185975 7.231619535492001 chr12 133851895 89050456 0.6652909620741642 1.6627953039587273 chr13 115169878 73629137 0.6393089779950969 1.4551166244661926 chr14 107349540 71768590 0.6685505126524063 1.572369552745376 chr15 102531392 59053074 0.5759511584510625 1.4099977908737165 chr16 90354753 64883644 0.7180988475503884 8.027819454915205 chr17 81195210 51747495 0.6373220169022286 10.015066247529573 chr18 78077248 86381613 1.106360882494219 10.114360326397508 chr19 59128983 27169223 0.45949078813007826 5.430430655896461 chr20 63025520 55502796 0.880640032799412 3.150861002992208 chr21 48129895 21361777 0.4438359360642694 4.062779923726896 chr22 51304566 11379007 0.2217932610520475 0.8279732004597365 chrMT 16571 6510403 392.87930722346266 233.9643324108201 chrX 155270560 73240806 0.47169795742348064 1.964109152002902 chrY 59373566 4043045 0.06809503407627562 8.492674866563412