BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617414.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,304,536 (94.7%) number of supplementary alignments = 464,163 (1.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,229,304 number of mapped paired reads (second in pair) = 15,075,232 number of mapped paired reads (both in pair) = 29,888,696 number of mapped paired reads (singletons) = 415,840 number of mapped bases = 2,990,244,533 bp number of sequenced bases = 2,989,591,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,396,184 duplication rate = 4.19% >>>>>>> Insert size mean insert size = 46,754.7625 std insert size = 2,047,940.4524 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.9588 >>>>>>> ACTG content number of A's = 891,347,018 bp (29.82%) number of C's = 601,005,041 bp (20.1%) number of T's = 882,949,133 bp (29.53%) number of G's = 613,029,631 bp (20.51%) number of N's = 1,260,441 bp (0.04%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 29,710,181 number of insertions = 242,893 mapped reads with insertion percentage = 0.79% number of deletions = 291,265 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.9659X std coverageData = 2.9514X There is a 29.77% of reference with a coverageData >= 1X There is a 17.14% of reference with a coverageData >= 2X There is a 11.01% of reference with a coverageData >= 3X There is a 7.63% of reference with a coverageData >= 4X There is a 5.55% of reference with a coverageData >= 5X There is a 4.18% of reference with a coverageData >= 6X There is a 3.24% of reference with a coverageData >= 7X There is a 2.57% of reference with a coverageData >= 8X There is a 2.07% of reference with a coverageData >= 9X There is a 1.7% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192426277 0.7720192480483329 2.7712904843107746 chr2 243199373 298040623 1.2254991422202393 3.088884287880734 chr3 198022430 252341672 1.2743085316143228 3.4459463044016236 chr4 191154276 143405757 0.7502095166314773 2.2931996040254825 chr5 180915260 191037811 1.0559518915098705 2.8887952754539663 chr6 171115067 137061615 0.8009909203378333 2.6234160575840284 chr7 159138663 224481550 1.4106034684984126 3.2706524341638232 chr8 146364022 132439089 0.9048609568818763 3.306378977454687 chr9 141213431 119427193 0.8457212048052285 2.6373472342933626 chr10 135534747 95758579 0.7065242022401828 2.4361981695788937 chr11 135006516 222451321 1.6477080335885417 3.88240266381637 chr12 133851895 142523893 1.0647880106590946 2.7983892911655093 chr13 115169878 129421415 1.1237436146281234 2.780329905999325 chr14 107349540 86571870 0.8064484486845496 2.908187287940319 chr15 102531392 68619954 0.6692579966143443 2.3654958876188488 chr16 90354753 75583320 0.8365173661644563 3.3625564291380674 chr17 81195210 92262158 1.136300503441028 3.741848776599817 chr18 78077248 42961464 0.5502430618456224 2.0205726126801253 chr19 59128983 42666872 0.7215898166217403 2.3612553440000013 chr20 63025520 101864114 1.6162359945622027 4.7766585834285475 chr21 48129895 40972643 0.8512930061451411 2.5603253827250985 chr22 51304566 24099051 0.4697252677276327 2.091843178014303 chrMT 16571 189250 11.420553979844307 5.514270495658123 chrX 155270560 131253301 0.8453199434586955 2.588270301788043 chrY 59373566 2383741 0.04014818648420073 0.5835167349934697