BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617661.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 = 30,745,931 (96.08%) number of supplementary alignments = 142,556 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,362,565 number of mapped paired reads (second in pair) = 15,383,366 number of mapped paired reads (both in pair) = 30,258,138 number of mapped paired reads (singletons) = 487,793 number of mapped bases = 2,997,031,154 bp number of sequenced bases = 2,995,192,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,208,961 duplication rate = 10.93% >>>>>>> Insert size mean insert size = 30,903.4446 std insert size = 1,609,198.5994 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 52.756 >>>>>>> ACTG content number of A's = 890,236,466 bp (29.72%) number of C's = 598,408,698 bp (19.98%) number of T's = 889,882,397 bp (29.71%) number of G's = 614,584,770 bp (20.52%) number of N's = 2,080,381 bp (0.07%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 40,512,244 number of insertions = 466,526 mapped reads with insertion percentage = 1.49% number of deletions = 1,106,182 mapped reads with deletion percentage = 3.52% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.9681X std coverageData = 10.9033X There is a 33.61% of reference with a coverageData >= 1X There is a 19.59% of reference with a coverageData >= 2X There is a 12.05% of reference with a coverageData >= 3X There is a 7.74% of reference with a coverageData >= 4X There is a 5.12% of reference with a coverageData >= 5X There is a 3.48% of reference with a coverageData >= 6X There is a 2.43% of reference with a coverageData >= 7X There is a 1.73% of reference with a coverageData >= 8X There is a 1.25% of reference with a coverageData >= 9X There is a 0.93% of reference with a coverageData >= 10X There is a 0.7% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183915539 0.7378739449559887 10.388963270161776 chr2 243199373 309813898 1.273909114889042 12.528984181427404 chr3 198022430 250682709 1.2659308796483308 2.5137233515269575 chr4 191154276 167600793 0.8767828609808341 8.873488925615776 chr5 180915260 198192746 1.0955004348444681 2.3570269170852165 chr6 171115067 145096689 0.8479480594189873 5.834759450350765 chr7 159138663 234567214 1.4739800471994666 13.762411932900525 chr8 146364022 133104208 0.909405236213036 4.175521362011158 chr9 141213431 123102356 0.871746795812928 21.2881277468185 chr10 135534747 127066626 0.9375206639814659 21.97542664741079 chr11 135006516 165161125 1.2233566933910065 12.280000251762132 chr12 133851895 127900191 0.955535153237838 2.1784362827568975 chr13 115169878 128440746 1.1152286364321755 2.3179057401772596 chr14 107349540 85695699 0.798286597222494 2.4879854024324852 chr15 102531392 63950058 0.6237119847158614 1.5953960324556906 chr16 90354753 82963608 0.9181986032323058 16.980677172239513 chr17 81195210 74204962 0.9139081233979196 13.200413666431793 chr18 78077248 55298664 0.7082558032783123 18.734697580869096 chr19 59128983 31845327 0.5385739003831674 6.224986931707664 chr20 63025520 81057055 1.2860989484894374 3.1082532291006197 chr21 48129895 43678884 0.9075208661892987 4.567249007096466 chr22 51304566 19354815 0.3772532643585758 1.2913261554762199 chrMT 16571 3195723 192.85034095709372 137.86226536705004 chrX 155270560 149002496 0.9596313428637083 4.443241446399295 chrY 59373566 12139023 0.20445164098784296 18.049001887485137