BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124956.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,035,486 number of mapped reads = 5,501,826 (91.16%) number of supplementary alignments = 7,675 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,834,041 number of mapped paired reads (second in pair) = 2,667,785 number of mapped paired reads (both in pair) = 5,263,226 number of mapped paired reads (singletons) = 238,600 number of mapped bases = 340,642,833 bp number of sequenced bases = 340,509,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 448,257 duplication rate = 4.77% >>>>>>> Insert size mean insert size = 26,222.3608 std insert size = 1,485,337.0518 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 51.6051 >>>>>>> ACTG content number of A's = 95,226,932 bp (27.97%) number of C's = 59,304,376 bp (17.42%) number of T's = 104,598,893 bp (30.72%) number of G's = 81,376,976 bp (23.9%) number of N's = 2,691 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 2,102,225 number of insertions = 36,616 mapped reads with insertion percentage = 0.66% number of deletions = 89,134 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.98% >>>>>>> Coverage mean coverageData = 0.11X std coverageData = 1.627X There is a 8.3% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 28418850 0.11401716828621261 1.7105573515536838 chr2 243199373 31301575 0.12870746586998807 2.45381611012799 chr3 198022430 21824364 0.11021157552707539 0.4394924359413558 chr4 191154276 17314972 0.09058113876563242 2.782718768141998 chr5 180915260 19046149 0.1052766306170082 1.1193117483522739 chr6 171115067 20325216 0.1187809837926195 0.9426904152688919 chr7 159138663 18226467 0.11453198522850477 1.499779138018587 chr8 146364022 16897785 0.11545040078223595 0.6667911089947047 chr9 141213431 13339898 0.09446621263667193 2.3913128832598747 chr10 135534747 15665901 0.11558586522465711 3.254059804483389 chr11 135006516 22648328 0.16775729550712945 1.4880058861193928 chr12 133851895 11209133 0.08374280394013099 0.36837195373447124 chr13 115169878 16516586 0.14341064075799403 0.5589533301511737 chr14 107349540 5668481 0.052803961712365045 0.41847243246810056 chr15 102531392 6904804 0.0673433166692987 0.32432212230915625 chr16 90354753 10543782 0.11669316388923115 2.2667162147637723 chr17 81195210 6581352 0.08105591450530149 1.0129119859690192 chr18 78077248 9910699 0.1269345328359934 1.686149008411284 chr19 59128983 4834728 0.08176578988344853 1.2706396048389732 chr20 63025520 7889887 0.12518559148738478 0.4665814076782016 chr21 48129895 2992835 0.06218245437684832 0.41695825264624187 chr22 51304566 1984006 0.03867113893917356 0.23301768637536377 chrMT 16571 270140 16.301973326896384 11.712566213148406 chrX 155270560 29455666 0.18970541485778114 0.8894570466347553 chrY 59373566 871229 0.014673684918975558 0.7440336893785059