BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472557.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 = 17,610,648 number of mapped reads = 17,412,165 (98.87%) number of supplementary alignments = 65,897 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,737,018 number of mapped paired reads (second in pair) = 8,675,147 number of mapped paired reads (both in pair) = 17,304,878 number of mapped paired reads (singletons) = 107,287 number of mapped bases = 1,710,670,156 bp number of sequenced bases = 1,710,451,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,142,757 duplication rate = 46.31% >>>>>>> Insert size mean insert size = 27,882.9046 std insert size = 1,633,864.5945 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 54.9877 >>>>>>> ACTG content number of A's = 472,939,846 bp (27.65%) number of C's = 385,277,251 bp (22.52%) number of T's = 469,110,995 bp (27.43%) number of G's = 382,858,219 bp (22.38%) number of N's = 264,850 bp (0.02%) GC percentage = 44.91% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,397,401 number of insertions = 93,884 mapped reads with insertion percentage = 0.53% number of deletions = 91,652 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.5526X std coverageData = 20.1585X There is a 5.39% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161192604 0.6467089363841545 17.83496835922553 chr2 243199373 129663526 0.5331573202699005 19.116001606387993 chr3 198022430 198748209 1.0036651353081567 24.033331457158738 chr4 191154276 67444452 0.3528273257146495 14.319628515125524 chr5 180915260 64673288 0.35747834649216437 15.295743314368682 chr6 171115067 116754391 0.682315082166318 26.851740873763283 chr7 159138663 70605896 0.44367531226525386 13.870528618594475 chr8 146364022 58889321 0.40234833803624226 13.807970784034065 chr9 141213431 123796498 0.8766623480736758 26.066485509447077 chr10 135534747 42293054 0.3120458401711555 10.442476252251982 chr11 135006516 76615407 0.5674941422827325 21.766324229937627 chr12 133851895 91033207 0.6801039835857385 32.53956251835255 chr13 115169878 31963486 0.2775333842065892 8.578267554430964 chr14 107349540 70084163 0.6528594626488385 32.027936613137996 chr15 102531392 61417952 0.5990160749987672 20.682825508639315 chr16 90354753 81064233 0.897177296251366 30.113529245783575 chr17 81195210 62693459 0.7721324817067411 21.37094294365137 chr18 78077248 32410868 0.41511283799347026 15.942817793673774 chr19 59128983 26406168 0.44658586466809347 11.836388058530407 chr20 63025520 32281554 0.512198138151022 17.907643194518407 chr21 48129895 5876578 0.12209829254769826 5.834160978120248 chr22 51304566 23034360 0.4489729042830223 15.143198893375866 chrMT 16571 1670 0.10077846840866574 0.4254656958443596 chrX 155270560 79603921 0.5126787782564834 18.337340688873702 chrY 59373566 2121891 0.03573797470746493 0.8145506296670494