BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094117.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 507,654 number of mapped reads = 404,641 (79.71%) number of supplementary alignments = 632 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,681 number of mapped paired reads (second in pair) = 201,960 number of mapped paired reads (both in pair) = 401,780 number of mapped paired reads (singletons) = 2,861 number of mapped bases = 60,114,833 bp number of sequenced bases = 60,066,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 403,743 duplication rate = 54.84% >>>>>>> Insert size mean insert size = 418.9711 std insert size = 65,765.292 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 6.3688 >>>>>>> ACTG content number of A's = 16,536,742 bp (27.53%) number of C's = 12,611,228 bp (21%) number of T's = 17,413,194 bp (28.99%) number of G's = 13,504,306 bp (22.48%) number of N's = 896 bp (0%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0174 number of mismatches = 1,018,896 number of insertions = 21,732 mapped reads with insertion percentage = 5.3% number of deletions = 44,768 mapped reads with deletion percentage = 10.84% homopolymer indels = 62.69% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 35.5413X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 4738 1.9008979720856944E-5 0.008877605837614495 chr2 243199373 279840 0.0011506608612843752 1.1398673267138064 chr3 198022430 1453 7.337552619670408E-6 0.0028619813989068663 chr4 191154276 1652 8.642234087402785E-6 0.0037289308534583067 chr5 180915260 1021 5.6435261458873065E-6 0.0031136979607147 chr6 171115067 1192 6.966072718774671E-6 0.0033392129372743114 chr7 159138663 1798 1.1298322897183068E-5 0.007037684736571039 chr8 146364022 3157 2.156950838642573E-5 0.016629784658367085 chr9 141213431 763 5.403168767990631E-6 0.002702031836963977 chr10 135534747 1843 1.3597989008678343E-5 0.00812843360537318 chr11 135006516 1374 1.01772865540801E-5 0.006806687532639729 chr12 133851895 1876 1.4015490778072286E-5 0.008750827456443474 chr13 115169878 641 5.565691404136071E-6 0.002809387436675504 chr14 107349540 2575 2.3987061332540408E-5 0.029318502742330162 chr15 102531392 703 6.856436709646934E-6 0.0033650134715468567 chr16 90354753 791 8.75438174237497E-6 0.0036700210230408486 chr17 81195210 754 9.286262083686956E-6 0.006599187887800221 chr18 78077248 405 5.18717053142037E-6 0.002311025219757232 chr19 59128983 432 7.306061732873031E-6 0.0029021047931097506 chr20 63025520 234 3.7127817430145755E-6 0.0021524474673490336 chr21 48129895 459 9.536692319814951E-6 0.0037725624786270943 chr22 51304566 1094 2.1323638133884614E-5 0.005201314020686613 chrMT 16571 59780006 3607.507452778951 14932.100627094464 chrX 155270560 25272 1.6276105399503938E-4 0.1572229956523286 chrY 59373566 760 1.2800309147676931E-5 0.005568384542796306