BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124880.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 = 2,718,926 number of mapped reads = 2,694,702 (99.11%) number of supplementary alignments = 26,584 (0.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,348,564 number of mapped paired reads (second in pair) = 1,346,138 number of mapped paired reads (both in pair) = 2,688,840 number of mapped paired reads (singletons) = 5,862 number of mapped bases = 364,296,728 bp number of sequenced bases = 364,048,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,445 duplication rate = 14.38% >>>>>>> Insert size mean insert size = 46,593.7837 std insert size = 2,047,289.1573 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 53.6177 >>>>>>> ACTG content number of A's = 107,303,487 bp (29.48%) number of C's = 72,036,307 bp (19.79%) number of T's = 108,192,417 bp (29.72%) number of G's = 76,484,289 bp (21.01%) number of N's = 31,776 bp (0.01%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 3,583,678 number of insertions = 69,762 mapped reads with insertion percentage = 2.47% number of deletions = 129,504 mapped reads with deletion percentage = 4.63% homopolymer indels = 46.05% >>>>>>> Coverage mean coverageData = 0.1177X std coverageData = 1.5519X There is a 6.48% of reference with a coverageData >= 1X There is a 3.62% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 33780831 0.1355295760727513 1.9117883543998662 chr2 243199373 30342501 0.12476389484770588 1.4956342893064587 chr3 198022430 42546635 0.21485765526662812 0.6755462373965031 chr4 191154276 21641379 0.11321420296138184 0.9897477798390857 chr5 180915260 19917223 0.11009144833885212 0.4744655996022296 chr6 171115067 15105161 0.08827487412315363 0.7513397476584294 chr7 159138663 26047786 0.16367980922398476 3.297826748142754 chr8 146364022 24062443 0.1644013513102284 0.6937121767345319 chr9 141213431 14966493 0.10598491159102282 2.787333538641855 chr10 135534747 17933203 0.1323144315162222 2.992732649802419 chr11 135006516 15919854 0.11791915287999877 1.1733085439399429 chr12 133851895 17296126 0.12921838723314302 0.5154186633658157 chr13 115169878 7484344 0.06498525595381806 0.3535715173777624 chr14 107349540 9672476 0.09010263108719423 0.45023704523914265 chr15 102531392 9055474 0.0883190389144429 0.4188915700062873 chr16 90354753 7407588 0.08198337944656879 1.1896088246309406 chr17 81195210 9674458 0.11915060014008215 1.5168521052702746 chr18 78077248 8785029 0.11251714455919348 2.624122256146572 chr19 59128983 3755273 0.06350985268933172 0.9799380739095064 chr20 63025520 6723638 0.10668119834632067 0.5439404603040322 chr21 48129895 4294589 0.08922913710906703 0.6617527051770322 chr22 51304566 2531517 0.049342918133251534 0.3171793764131452 chrMT 16571 149106 8.998008569187133 5.632879539574812 chrX 155270560 10895201 0.07016913573313575 0.5490585108692937 chrY 59373566 4308400 0.07256427885769906 1.7946257138059944