BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008751.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,353,983 number of mapped reads = 1,120,355 (47.59%) number of supplementary alignments = 21,670 (0.92%) number of secondary alignments = 0 number of mapped bases = 74,360,753 bp number of sequenced bases = 74,316,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,237 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1245 >>>>>>> ACTG content number of A's = 23,877,228 bp (32.13%) number of C's = 13,577,278 bp (18.27%) number of T's = 21,216,325 bp (28.55%) number of G's = 15,640,148 bp (21.05%) number of N's = 5,903 bp (0.01%) GC percentage = 39.31% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 784,723 number of insertions = 5,842 mapped reads with insertion percentage = 0.52% number of deletions = 28,991 mapped reads with deletion percentage = 2.55% homopolymer indels = 49.59% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2213X There is a 2% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 5663301 0.022721311494746488 0.2569578377933014 chr2 243199373 6705239 0.02757095512742132 0.2778445370461125 chr3 198022430 5986749 0.03023268121697123 0.2092024465096194 chr4 191154276 3838696 0.020081664299259516 0.16902397981634348 chr5 180915260 3977907 0.02198768086229984 0.1763077203397673 chr6 171115067 3967600 0.023186736677022136 0.19599287816495858 chr7 159138663 4243131 0.02666310574696735 0.2853496297236027 chr8 146364022 6280470 0.04290993041992246 0.3048765333483123 chr9 141213431 2496020 0.017675514165504554 0.2085944542325422 chr10 135534747 3997615 0.029495130130725813 0.22779535757662286 chr11 135006516 3442188 0.02549645825983688 0.2299703284893144 chr12 133851895 3328444 0.02486661843674309 0.18799822584109097 chr13 115169878 2279305 0.019790808495950652 0.16841864544847499 chr14 107349540 2708536 0.02523099772947327 0.19265892926703387 chr15 102531392 2104115 0.020521666183952715 0.17010481884124143 chr16 90354753 1912815 0.02117005399815547 0.17892705272229018 chr17 81195210 1842901 0.02269716403221323 0.21273460338051042 chr18 78077248 1416772 0.01814577276084321 0.340456711720975 chr19 59128983 1197900 0.020259100346779177 0.18693493513365075 chr20 63025520 1674303 0.026565476968694587 0.19368406635956184 chr21 48129895 811275 0.016855947846967045 0.164612696725205 chr22 51304566 855558 0.016676059592824546 0.15079013813540199 chrMT 16571 21787 1.3147667612093417 1.75006140757784 chrX 155270560 3459447 0.02228012187242707 0.1837527143478789 chrY 59373566 148679 0.0025041278470624454 0.06779945121991167