BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777274.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 12,625,652 number of mapped reads = 12,330,507 (97.66%) number of supplementary alignments = 84,320 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,183,997 number of mapped paired reads (second in pair) = 6,146,510 number of mapped paired reads (both in pair) = 12,276,932 number of mapped paired reads (singletons) = 53,575 number of mapped bases = 1,185,968,238 bp number of sequenced bases = 1,185,160,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 893,678 duplication rate = 7.05% >>>>>>> Insert size mean insert size = 84,570.8187 std insert size = 3,003,143.1014 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 54.0624 >>>>>>> ACTG content number of A's = 323,774,502 bp (27.32%) number of C's = 266,739,219 bp (22.51%) number of T's = 318,244,135 bp (26.85%) number of G's = 276,380,593 bp (23.32%) number of N's = 22,155 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 8,646,183 number of insertions = 194,132 mapped reads with insertion percentage = 1.55% number of deletions = 584,724 mapped reads with deletion percentage = 4.63% homopolymer indels = 54.17% >>>>>>> Coverage mean coverageData = 0.3831X std coverageData = 2.9519X There is a 17.15% of reference with a coverageData >= 1X There is a 8.95% of reference with a coverageData >= 2X There is a 4.38% of reference with a coverageData >= 3X There is a 2.56% of reference with a coverageData >= 4X There is a 1.56% of reference with a coverageData >= 5X There is a 1.02% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 118901714 0.4770367813847894 1.431875849912062 chr2 243199373 110218293 0.4532013863374557 1.5414541825625336 chr3 198022430 71804976 0.36261031641718566 1.1395848759729785 chr4 191154276 49587804 0.25941247581613086 0.9059336671160384 chr5 180915260 67103946 0.37091368633027416 1.1116979927153516 chr6 171115067 53840011 0.31464214077653374 11.408662277386439 chr7 159138663 71319351 0.44815854083177764 1.2891063475270692 chr8 146364022 53181752 0.3633526277379833 1.2288674155752888 chr9 141213431 47630365 0.33729344767495945 1.2337451345257118 chr10 135534747 57799457 0.4264549001592927 1.2555289888500638 chr11 135006516 68228670 0.5053731628775606 1.4377853033494667 chr12 133851895 55066962 0.4114021844815869 1.1979643196373961 chr13 115169878 37097493 0.32211107317487997 1.0881178150448838 chr14 107349540 24694401 0.2300373247989698 0.8260513292896532 chr15 102531392 52155395 0.5086773326943616 1.4739716442174617 chr16 90354753 42778587 0.4734514298323631 1.6718121581381526 chr17 81195210 47705843 0.5875450411422053 1.6450420743966483 chr18 78077248 21190759 0.27140760647711354 1.0597720778885367 chr19 59128983 26261356 0.4441367780670268 1.359090110652806 chr20 63025520 46026860 0.7302892542576404 1.7918925207483523 chr21 48129895 10556339 0.21933018968771903 1.0291582584328487 chr22 51304566 20642055 0.4023434288480289 1.3341439538058653 chrMT 16571 225547 13.610946834831935 12.805071559348113 chrX 155270560 30887227 0.19892519869832376 0.7227621016218316 chrY 59373566 1063075 0.017904853483114016 0.5007802056205226