BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695952.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 89,012,154 number of mapped reads = 88,164,933 (99.05%) number of supplementary alignments = 1,415,294 (1.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 44,192,664 number of mapped paired reads (second in pair) = 43,972,269 number of mapped paired reads (both in pair) = 87,666,846 number of mapped paired reads (singletons) = 498,087 number of mapped bases = 8,730,461,532 bp number of sequenced bases = 8,727,484,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,237,242 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 87,813.2728 std insert size = 2,841,237.6009 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 53.9058 >>>>>>> ACTG content number of A's = 2,445,556,083 bp (28.02%) number of C's = 1,893,641,595 bp (21.7%) number of T's = 2,434,162,402 bp (27.89%) number of G's = 1,953,986,931 bp (22.39%) number of N's = 137,891 bp (0%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 35,456,015 number of insertions = 1,331,867 mapped reads with insertion percentage = 1.46% number of deletions = 1,128,478 mapped reads with deletion percentage = 1.23% homopolymer indels = 41.42% >>>>>>> Coverage mean coverageData = 2.8202X std coverageData = 10.6203X There is a 70.17% of reference with a coverageData >= 1X There is a 50.61% of reference with a coverageData >= 2X There is a 36.22% of reference with a coverageData >= 3X There is a 26.17% of reference with a coverageData >= 4X There is a 19.21% of reference with a coverageData >= 5X There is a 14.35% of reference with a coverageData >= 6X There is a 10.91% of reference with a coverageData >= 7X There is a 8.43% of reference with a coverageData >= 8X There is a 6.62% of reference with a coverageData >= 9X There is a 5.26% of reference with a coverageData >= 10X There is a 4.24% of reference with a coverageData >= 11X There is a 3.45% of reference with a coverageData >= 12X There is a 2.84% of reference with a coverageData >= 13X There is a 2.36% of reference with a coverageData >= 14X There is a 1.98% of reference with a coverageData >= 15X There is a 1.67% of reference with a coverageData >= 16X There is a 1.42% of reference with a coverageData >= 17X There is a 1.22% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 0.91% of reference with a coverageData >= 20X There is a 0.79% of reference with a coverageData >= 21X There is a 0.69% of reference with a coverageData >= 22X There is a 0.61% of reference with a coverageData >= 23X There is a 0.54% of reference with a coverageData >= 24X There is a 0.48% of reference with a coverageData >= 25X There is a 0.43% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 770298787 3.0904588478437534 8.89665125019009 chr2 243199373 691072202 2.8415871039272784 22.47046392948267 chr3 198022430 510781938 2.5794145541997437 4.592649850528783 chr4 191154276 494428365 2.586540962337667 6.328157351063962 chr5 180915260 444447872 2.456663257704187 5.148557108098547 chr6 171115067 557126821 3.2558606951893956 7.827621089243083 chr7 159138663 433661789 2.725056129194701 5.913529254231158 chr8 146364022 383300541 2.6188166720370667 7.165371555294614 chr9 141213431 327250435 2.3174172079991457 14.078734247517186 chr10 135534747 396701820 2.926938137863643 15.127590967135221 chr11 135006516 463698218 3.434635836391778 7.220002032074621 chr12 133851895 474849085 3.547570880486974 5.400151633274049 chr13 115169878 239250132 2.0773672435426214 4.815921494140264 chr14 107349540 289750071 2.6991272715281314 10.281237552760565 chr15 102531392 259363906 2.5296048453141062 5.423903671261211 chr16 90354753 315161436 3.488044906724497 16.300053380097864 chr17 81195210 367547732 4.526716933178694 9.066205268594087 chr18 78077248 230939707 2.957836154778406 11.178802725863797 chr19 59128983 308845859 5.223256740268981 9.780615717581611 chr20 63025520 241804730 3.8366161834126875 6.045220860270774 chr21 48129895 110878943 2.3037437127174285 6.457476878207731 chr22 51304566 152372163 2.9699532591309707 6.361385982629273 chrMT 16571 5727240 345.61824874781246 121.01698476978382 chrX 155270560 197899848 1.2745484269522824 3.490478039690173 chrY 59373566 63301892 1.06616287793797 18.949512609856118