BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124850.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 = 78,782,492 number of mapped reads = 74,520,794 (94.59%) number of supplementary alignments = 1,704,978 (2.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 37,794,715 number of mapped paired reads (second in pair) = 36,726,079 number of mapped paired reads (both in pair) = 73,109,754 number of mapped paired reads (singletons) = 1,411,040 number of mapped bases = 9,128,682,750 bp number of sequenced bases = 9,122,017,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,253,455 duplication rate = 33.49% >>>>>>> Insert size mean insert size = 93,545.7283 std insert size = 2,878,588.5046 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.9623 >>>>>>> ACTG content number of A's = 2,660,240,565 bp (29.16%) number of C's = 1,806,977,609 bp (19.81%) number of T's = 2,691,090,290 bp (29.5%) number of G's = 1,963,569,862 bp (21.53%) number of N's = 138,903 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 107,809,977 number of insertions = 1,661,847 mapped reads with insertion percentage = 2.07% number of deletions = 3,048,639 mapped reads with deletion percentage = 3.91% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 2.9488X std coverageData = 43.4369X There is a 48.67% of reference with a coverageData >= 1X There is a 38.34% of reference with a coverageData >= 2X There is a 28.55% of reference with a coverageData >= 3X There is a 23.51% of reference with a coverageData >= 4X There is a 18.64% of reference with a coverageData >= 5X There is a 15.63% of reference with a coverageData >= 6X There is a 12.83% of reference with a coverageData >= 7X There is a 10.89% of reference with a coverageData >= 8X There is a 9.15% of reference with a coverageData >= 9X There is a 7.85% of reference with a coverageData >= 10X There is a 6.71% of reference with a coverageData >= 11X There is a 5.81% of reference with a coverageData >= 12X There is a 5.02% of reference with a coverageData >= 13X There is a 4.39% of reference with a coverageData >= 14X There is a 3.83% of reference with a coverageData >= 15X There is a 3.37% of reference with a coverageData >= 16X There is a 2.97% of reference with a coverageData >= 17X There is a 2.63% of reference with a coverageData >= 18X There is a 2.33% of reference with a coverageData >= 19X There is a 2.08% of reference with a coverageData >= 20X There is a 1.85% of reference with a coverageData >= 21X There is a 1.66% of reference with a coverageData >= 22X There is a 1.49% of reference with a coverageData >= 23X There is a 1.34% of reference with a coverageData >= 24X There is a 1.21% of reference with a coverageData >= 25X There is a 1.09% of reference with a coverageData >= 26X There is a 0.99% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.74% of reference with a coverageData >= 30X There is a 0.68% of reference with a coverageData >= 31X There is a 0.62% of reference with a coverageData >= 32X There is a 0.57% of reference with a coverageData >= 33X There is a 0.52% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.44% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.38% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.32% of reference with a coverageData >= 40X There is a 0.3% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 751174807 3.0137329407095037 34.75392096808865 chr2 243199373 788464984 3.2420518781518406 49.62959541333455 chr3 198022430 667554270 3.3711043238889653 8.133849990289121 chr4 191154276 528891248 2.766829280868402 31.456679685140426 chr5 180915260 532992537 2.9460894398847284 7.03223806490346 chr6 171115067 513679660 3.0019545853317524 15.84915707509011 chr7 159138663 595781297 3.7437872467233184 36.33927361497541 chr8 146364022 589763646 4.029430442954075 14.547130883627265 chr9 141213431 362351535 2.5659849239127968 48.56644735314252 chr10 135534747 479395814 3.537069457177649 146.52301474915987 chr11 135006516 348881350 2.5841815664660217 18.180254391098366 chr12 133851895 422489907 3.156398398393986 6.461862811789178 chr13 115169878 252340203 2.1910260510999238 4.8531777637794145 chr14 107349540 291854731 2.7187329447336244 7.786415391077511 chr15 102531392 247686263 2.415711502288002 6.110288241436441 chr16 90354753 332721786 3.6823938415281816 72.0537831610188 chr17 81195210 186459663 2.2964367356153152 36.24017346628704 chr18 78077248 178051607 2.2804544417344217 46.93134107623884 chr19 59128983 123186641 2.0833546384520094 19.97901554314367 chr20 63025520 181743596 2.883650876660756 11.912945672398859 chr21 48129895 98764308 2.0520366395979046 17.173275771242484 chr22 51304566 70101060 1.3663707826706886 6.613779756844029 chrMT 16571 2403478 145.0412165831875 82.9052482659991 chrX 155270560 412401510 2.6560186940782593 10.747191335836282 chrY 59373566 169546849 2.8555948450190782 73.80064935802757