BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124977.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 = 2,851,354 number of mapped reads = 2,794,345 (98%) number of supplementary alignments = 58,175 (2.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,412,245 number of mapped paired reads (second in pair) = 1,382,100 number of mapped paired reads (both in pair) = 2,761,624 number of mapped paired reads (singletons) = 32,721 number of mapped bases = 355,995,556 bp number of sequenced bases = 355,687,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 497,964 duplication rate = 15.06% >>>>>>> Insert size mean insert size = 74,786.5298 std insert size = 2,535,659.9892 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.2107 >>>>>>> ACTG content number of A's = 101,988,074 bp (28.67%) number of C's = 70,933,001 bp (19.94%) number of T's = 104,156,067 bp (29.28%) number of G's = 78,607,491 bp (22.1%) number of N's = 2,621 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 3,998,925 number of insertions = 79,278 mapped reads with insertion percentage = 2.63% number of deletions = 139,781 mapped reads with deletion percentage = 4.77% homopolymer indels = 45.49% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 1.5452X There is a 6.36% of reference with a coverageData >= 1X There is a 2.97% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 34523662 0.13850983344189943 1.1561793141669994 chr2 243199373 28745780 0.11819841328291582 1.8520587317457546 chr3 198022430 24572257 0.12408825101277668 0.5398043368818953 chr4 191154276 17601521 0.09208018448930748 1.850746489578589 chr5 180915260 19305171 0.10670836169375651 0.5015452845941601 chr6 171115067 18654727 0.10901861143530979 0.678677300925705 chr7 159138663 24736862 0.1554421881752268 1.293722671811708 chr8 146364022 23039751 0.15741403307433025 0.7165679058854495 chr9 141213431 13274012 0.09399964228615053 1.5978429104110172 chr10 135534747 19294945 0.1423616115209187 4.540427412526507 chr11 135006516 12438073 0.0921294272937167 0.6126223256467055 chr12 133851895 17800083 0.13298342171397723 0.5483499244599138 chr13 115169878 8006125 0.06951578953656615 0.38125038542677175 chr14 107349540 11224199 0.10455749507636455 0.49872675489590024 chr15 102531392 12303293 0.1199953766354796 0.5240896479955508 chr16 90354753 13711936 0.1517566651972365 2.432038445331618 chr17 81195210 7920717 0.09755153044126617 1.300333092392867 chr18 78077248 5386197 0.0689854872958637 1.4722216228085274 chr19 59128983 6026204 0.1019162463863111 0.7803014345655691 chr20 63025520 7791951 0.12363168126181268 0.8156382135505922 chr21 48129895 3579423 0.07437005628206751 1.122056358806245 chr22 51304566 2860514 0.055755544253117746 0.3901113166366189 chrMT 16571 324811 19.601170719932412 12.275387307438432 chrX 155270560 15957689 0.10277343625217814 0.5493245062441003 chrY 59373566 6915653 0.11647696889218344 3.3923073048784915