BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472414.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,256,516 number of mapped reads = 18,100,468 (99.15%) number of supplementary alignments = 71,951 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,082,260 number of mapped paired reads (second in pair) = 9,018,208 number of mapped paired reads (both in pair) = 17,998,378 number of mapped paired reads (singletons) = 102,090 number of mapped bases = 1,776,053,268 bp number of sequenced bases = 1,775,843,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,626,725 duplication rate = 47.1% >>>>>>> Insert size mean insert size = 19,713.1045 std insert size = 1,443,213.2619 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 55.157 >>>>>>> ACTG content number of A's = 478,547,873 bp (26.95%) number of C's = 410,109,710 bp (23.09%) number of T's = 479,966,501 bp (27.03%) number of G's = 407,002,351 bp (22.92%) number of N's = 217,457 bp (0.01%) GC percentage = 46.01% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,935,851 number of insertions = 104,333 mapped reads with insertion percentage = 0.57% number of deletions = 87,929 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.5737X std coverageData = 19.4546X There is a 4.73% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 298949192 1.1993919646041724 33.89873135064966 chr2 243199373 136625321 0.5617831958801967 19.842542817310125 chr3 198022430 126139869 0.6369978845325754 14.247111876168772 chr4 191154276 68091067 0.3562100122730187 19.5713290086166 chr5 180915260 70952811 0.39218809402811017 11.919207568615148 chr6 171115067 134118340 0.7837903602024713 21.39997883862521 chr7 159138663 105496883 0.6629242762960752 25.47404188119363 chr8 146364022 112696803 0.7699761284231449 24.227188646271216 chr9 141213431 69093705 0.4892856473404431 13.900735972924666 chr10 135534747 34651828 0.2556674857702726 7.788031650828387 chr11 135006516 69751264 0.51665109260356 17.50428095954831 chr12 133851895 65133744 0.4866105481734121 20.159882639662843 chr13 115169878 50546962 0.43889047099624434 18.921822954170686 chr14 107349540 35348998 0.3292887701242129 9.597627782069408 chr15 102531392 48165439 0.46976285077647245 17.605131529844368 chr16 90354753 62492218 0.6916317728188577 19.224121531331296 chr17 81195210 76599742 0.9434022277915163 19.799965954740408 chr18 78077248 13350700 0.1709934755897134 5.313315466729313 chr19 59128983 43008311 0.72736429442732 16.15068926636017 chr20 63025520 41518574 0.6587581347999985 20.430403207856376 chr21 48129895 8807425 0.1829928155879002 7.213164805430065 chr22 51304566 22670746 0.4418855428969032 12.617692898503032 chrMT 16571 11152 0.67298292197212 1.2197765005291696 chrX 155270560 80898107 0.5210138161413214 17.693806324636782 chrY 59373566 934067 0.015732034690319932 0.44363591625493887