BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365333.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 = 109,538,278 number of mapped reads = 107,116,257 (97.79%) number of supplementary alignments = 857,388 (0.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,858,758 number of mapped paired reads (second in pair) = 53,257,499 number of mapped paired reads (both in pair) = 106,362,666 number of mapped paired reads (singletons) = 753,591 number of mapped bases = 14,078,157,215 bp number of sequenced bases = 14,072,922,384 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,283,927 duplication rate = 31.29% >>>>>>> Insert size mean insert size = 89,601.1827 std insert size = 2,963,393.2936 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 54.2315 >>>>>>> ACTG content number of A's = 4,175,086,307 bp (29.67%) number of C's = 2,817,890,988 bp (20.02%) number of T's = 4,120,068,160 bp (29.28%) number of G's = 2,959,047,865 bp (21.03%) number of N's = 829,064 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 107,305,598 number of insertions = 4,075,777 mapped reads with insertion percentage = 3.69% number of deletions = 2,169,691 mapped reads with deletion percentage = 1.96% homopolymer indels = 50.08% >>>>>>> Coverage mean coverageData = 4.5477X std coverageData = 52.3185X There is a 68.13% of reference with a coverageData >= 1X There is a 60.44% of reference with a coverageData >= 2X There is a 50.96% of reference with a coverageData >= 3X There is a 44% of reference with a coverageData >= 4X There is a 36.78% of reference with a coverageData >= 5X There is a 31.2% of reference with a coverageData >= 6X There is a 25.86% of reference with a coverageData >= 7X There is a 21.66% of reference with a coverageData >= 8X There is a 17.83% of reference with a coverageData >= 9X There is a 14.79% of reference with a coverageData >= 10X There is a 12.11% of reference with a coverageData >= 11X There is a 9.98% of reference with a coverageData >= 12X There is a 8.13% of reference with a coverageData >= 13X There is a 6.66% of reference with a coverageData >= 14X There is a 5.41% of reference with a coverageData >= 15X There is a 4.42% of reference with a coverageData >= 16X There is a 3.58% of reference with a coverageData >= 17X There is a 2.92% of reference with a coverageData >= 18X There is a 2.37% of reference with a coverageData >= 19X There is a 1.93% of reference with a coverageData >= 20X There is a 1.56% of reference with a coverageData >= 21X There is a 1.28% of reference with a coverageData >= 22X There is a 1.04% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.7% of reference with a coverageData >= 25X There is a 0.58% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1192240686 4.783300764574625 149.01966243782968 chr2 243199373 1277722268 5.253805765362726 28.98586312480332 chr3 198022430 946629147 4.780413749088929 6.7472662544888 chr4 191154276 913353044 4.7780937110713655 20.30434322437457 chr5 180915260 861996520 4.764642407721714 6.385809470660234 chr6 171115067 852681023 4.983085580651995 18.199442029783196 chr7 159138663 757141446 4.757746682840989 31.323698531097634 chr8 146364022 724285167 4.948519158622192 17.05110453092655 chr9 141213431 597599763 4.231890400000267 48.87512399856872 chr10 135534747 726045956 5.356899039329007 90.70108247135964 chr11 135006516 652818084 4.835456119762397 30.036864764625342 chr12 133851895 654336602 4.888512052817781 22.864839267961234 chr13 115169878 455328389 3.9535371306028475 5.16059990278713 chr14 107349540 425016102 3.959179536307282 5.692344500469349 chr15 102531392 423775757 4.133131802209415 12.453301707248153 chr16 90354753 404445441 4.476194417796704 14.35246556839807 chr17 81195210 408938450 5.036484910870974 22.39209307641472 chr18 78077248 384605342 4.925959249998155 47.49826737773339 chr19 59128983 275061875 4.65189592386529 75.57971939756817 chr20 63025520 292566090 4.6420258016117915 9.211175954307738 chr21 48129895 196604738 4.084877766718585 15.286071518373662 chr22 51304566 172164583 3.3557360762003134 13.25858728219614 chrMT 16571 20349120 1227.9958964455977 266.47599063849043 chrX 155270560 354630722 2.283953390778007 10.070425925409905 chrY 59373566 107820900 1.8159748060273153 35.47380262950655