BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975228.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 107,116,602 number of mapped reads = 106,518,911 (99.44%) number of supplementary alignments = 226,958 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,241,515 number of mapped paired reads (second in pair) = 53,277,396 number of mapped paired reads (both in pair) = 106,275,236 number of mapped paired reads (singletons) = 243,675 number of mapped bases = 9,677,249,828 bp number of sequenced bases = 9,673,997,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,343,252 duplication rate = 45.14% >>>>>>> Insert size mean insert size = 63,123.4222 std insert size = 2,461,176.333 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 55.6439 >>>>>>> ACTG content number of A's = 2,585,340,078 bp (26.72%) number of C's = 2,087,237,094 bp (21.58%) number of T's = 2,715,470,613 bp (28.07%) number of G's = 2,285,675,161 bp (23.63%) number of N's = 274,475 bp (0%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 59,646,712 number of insertions = 803,334 mapped reads with insertion percentage = 0.74% number of deletions = 2,184,291 mapped reads with deletion percentage = 2.02% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 3.126X std coverageData = 39.0836X There is a 25.42% of reference with a coverageData >= 1X There is a 14.93% of reference with a coverageData >= 2X There is a 9.1% of reference with a coverageData >= 3X There is a 6.46% of reference with a coverageData >= 4X There is a 4.76% of reference with a coverageData >= 5X There is a 3.85% of reference with a coverageData >= 6X There is a 3.22% of reference with a coverageData >= 7X There is a 2.82% of reference with a coverageData >= 8X There is a 2.54% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.19% of reference with a coverageData >= 11X There is a 2.07% of reference with a coverageData >= 12X There is a 1.98% of reference with a coverageData >= 13X There is a 1.9% of reference with a coverageData >= 14X There is a 1.83% of reference with a coverageData >= 15X There is a 1.78% of reference with a coverageData >= 16X There is a 1.72% of reference with a coverageData >= 17X There is a 1.68% of reference with a coverageData >= 18X There is a 1.64% of reference with a coverageData >= 19X There is a 1.6% of reference with a coverageData >= 20X There is a 1.56% of reference with a coverageData >= 21X There is a 1.53% of reference with a coverageData >= 22X There is a 1.5% of reference with a coverageData >= 23X There is a 1.47% of reference with a coverageData >= 24X There is a 1.44% of reference with a coverageData >= 25X There is a 1.42% of reference with a coverageData >= 26X There is a 1.39% of reference with a coverageData >= 27X There is a 1.37% of reference with a coverageData >= 28X There is a 1.35% of reference with a coverageData >= 29X There is a 1.32% of reference with a coverageData >= 30X There is a 1.3% of reference with a coverageData >= 31X There is a 1.28% of reference with a coverageData >= 32X There is a 1.26% of reference with a coverageData >= 33X There is a 1.24% of reference with a coverageData >= 34X There is a 1.23% of reference with a coverageData >= 35X There is a 1.21% of reference with a coverageData >= 36X There is a 1.19% of reference with a coverageData >= 37X There is a 1.17% of reference with a coverageData >= 38X There is a 1.16% of reference with a coverageData >= 39X There is a 1.14% of reference with a coverageData >= 40X There is a 1.13% of reference with a coverageData >= 41X There is a 1.11% of reference with a coverageData >= 42X There is a 1.1% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 1.07% of reference with a coverageData >= 45X There is a 1.06% of reference with a coverageData >= 46X There is a 1.05% of reference with a coverageData >= 47X There is a 1.03% of reference with a coverageData >= 48X There is a 1.02% of reference with a coverageData >= 49X There is a 1.01% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 968085382 3.8839838316792 43.81753571090351 chr2 243199373 811601169 3.3371844630536938 40.00804475607977 chr3 198022430 611861612 3.089860133521238 38.20167180608149 chr4 191154276 475620105 2.4881478717222105 34.77587329878648 chr5 180915260 478428378 2.6444887954725322 33.48502724794759 chr6 171115067 704936780 4.119665160754079 50.67713538035482 chr7 159138663 485197829 3.0488997447465045 39.95414670408257 chr8 146364022 357100541 2.4398109324981516 30.575195416887432 chr9 141213431 392297011 2.778043194772316 34.80916456350015 chr10 135534747 436215065 3.21847404193701 39.12925966540127 chr11 135006516 521849020 3.8653617281702166 43.520395610376646 chr12 133851895 533261383 3.983965882589858 43.53469609326177 chr13 115169878 224131803 1.9460974248839613 31.206666215705336 chr14 107349540 322111105 3.0005820704960637 38.52452870609214 chr15 102531392 340384776 3.3198103464741804 38.67065774976415 chr16 90354753 291560394 3.2268406953644155 35.98631404029153 chr17 81195210 377846316 4.653554267548541 46.86416959243061 chr18 78077248 241031373 3.0870884819096083 42.37672607911319 chr19 59128983 337735354 5.711841078003997 59.15787804043863 chr20 63025520 227948490 3.6167649231612846 46.39498131191108 chr21 48129895 98433820 2.0451700549107783 29.174576970758558 chr22 51304566 141963520 2.7670737922234836 37.60671558497125 chrMT 16571 395508 23.867479331362016 31.9256568187178 chrX 155270560 273807248 1.7634202388398676 24.95185138774103 chrY 59373566 23445846 0.39488694345897973 8.363628899054499