BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695936.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 11,423,104 number of mapped reads = 10,398,667 (91.03%) number of supplementary alignments = 20,353 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,273,766 number of mapped paired reads (second in pair) = 5,124,901 number of mapped paired reads (both in pair) = 10,019,476 number of mapped paired reads (singletons) = 379,191 number of mapped bases = 888,304,404 bp number of sequenced bases = 887,993,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,139,468 duplication rate = 7.69% >>>>>>> Insert size mean insert size = 63,287.4565 std insert size = 2,384,995.225 median insert size = 284 >>>>>>> Mapping quality mean mapping quality = 52.9997 >>>>>>> ACTG content number of A's = 225,438,606 bp (25.39%) number of C's = 170,504,267 bp (19.2%) number of T's = 263,481,690 bp (29.67%) number of G's = 228,268,120 bp (25.71%) number of N's = 300,920 bp (0.03%) GC percentage = 44.91% >>>>>>> Mismatches and indels general error rate = 0.015 number of mismatches = 13,192,830 number of insertions = 85,580 mapped reads with insertion percentage = 0.81% number of deletions = 208,404 mapped reads with deletion percentage = 1.97% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.2869X std coverageData = 2.6628X There is a 13.55% of reference with a coverageData >= 1X There is a 5.64% of reference with a coverageData >= 2X There is a 2.96% of reference with a coverageData >= 3X There is a 1.75% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.52% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 75131868 0.30143101629423824 1.7494721687076449 chr2 243199373 71752790 0.2950369037341227 4.665733689357339 chr3 198022430 54367492 0.27455219088059873 1.056500325629635 chr4 191154276 45485324 0.23795085808072639 1.151306220638084 chr5 180915260 43878199 0.24253453799309135 1.1824835099447428 chr6 171115067 47430514 0.277184907393339 2.7571606983285504 chr7 159138663 49018710 0.30802514659809604 2.9760475530222044 chr8 146364022 42784647 0.29231669378421427 2.1218468650355238 chr9 141213431 58452585 0.41393077546568496 3.5833005056357305 chr10 135534747 36915463 0.272368996269274 1.1107544200221717 chr11 135006516 51519975 0.3816110253522874 5.647068940557821 chr12 133851895 42976631 0.3210759997084838 1.3132757934078128 chr13 115169878 22676245 0.19689388747984954 0.8707180024335558 chr14 107349540 27632817 0.2574097383183943 1.540200504956157 chr15 102531392 35225738 0.3435605165684281 1.2537639374838945 chr16 90354753 32671125 0.36158723160916617 1.829417193703371 chr17 81195210 29689226 0.36565243195996416 1.5730675989356389 chr18 78077248 29841383 0.38220331485044146 5.479084682886611 chr19 59128983 20533373 0.34726409889376925 1.381956282646073 chr20 63025520 19780130 0.3138431860617731 1.207440062888761 chr21 48129895 10559635 0.21939867103387614 2.0095901648901293 chr22 51304566 14650235 0.28555421363470845 1.1421669808660213 chrMT 16571 269379 16.256049725423935 49.70936796156086 chrX 155270560 21530224 0.13866262863996884 2.9646220389312785 chrY 59373566 3530696 0.05946578987692941 0.8156680234236389