BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354859.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 36,656,616 number of mapped reads = 36,182,431 (98.71%) number of supplementary alignments = 921,022 (2.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,119,149 number of mapped paired reads (second in pair) = 18,063,282 number of mapped paired reads (both in pair) = 36,067,860 number of mapped paired reads (singletons) = 114,571 number of mapped bases = 4,819,286,857 bp number of sequenced bases = 4,816,686,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,902,444 duplication rate = 67.15% >>>>>>> Insert size mean insert size = 229,825.8314 std insert size = 5,504,578.5948 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 53.8535 >>>>>>> ACTG content number of A's = 1,320,571,253 bp (27.42%) number of C's = 1,064,309,314 bp (22.1%) number of T's = 1,333,877,923 bp (27.69%) number of G's = 1,097,814,189 bp (22.79%) number of N's = 114,166 bp (0%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 36,990,491 number of insertions = 852,530 mapped reads with insertion percentage = 2.16% number of deletions = 837,534 mapped reads with deletion percentage = 2.18% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 1.5568X std coverageData = 40.1948X There is a 34.71% of reference with a coverageData >= 1X There is a 28.13% of reference with a coverageData >= 2X There is a 20.14% of reference with a coverageData >= 3X There is a 16.14% of reference with a coverageData >= 4X There is a 11.3% of reference with a coverageData >= 5X There is a 9.09% of reference with a coverageData >= 6X There is a 6.32% of reference with a coverageData >= 7X There is a 5.11% of reference with a coverageData >= 8X There is a 3.55% of reference with a coverageData >= 9X There is a 2.88% of reference with a coverageData >= 10X There is a 2.01% of reference with a coverageData >= 11X There is a 1.63% of reference with a coverageData >= 12X There is a 1.15% of reference with a coverageData >= 13X There is a 0.93% of reference with a coverageData >= 14X There is a 0.67% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 411109426 1.6493817521923044 36.01134967582114 chr2 243199373 435588144 1.791074288666032 123.58261941464059 chr3 198022430 306850465 1.5495742830749022 3.816396201419014 chr4 191154276 290405025 1.5192180424988244 30.56380904620589 chr5 180915260 263321388 1.4554957276683018 3.0217000966484826 chr6 171115067 259665137 1.517488445362909 5.90369958882219 chr7 159138663 246830323 1.551039315945491 21.699092617739524 chr8 146364022 228625308 1.5620321502233656 4.471384939177141 chr9 141213431 207221537 1.4674350416427457 19.996022809411112 chr10 135534747 276827905 2.0424866030848903 57.95364433451268 chr11 135006516 242102869 1.7932680301149317 6.909845410987641 chr12 133851895 223281483 1.668123435981239 3.182864729288712 chr13 115169878 136033544 1.1811555795865305 2.6045097978921925 chr14 107349540 138389898 1.2891522217980627 6.55721399658529 chr15 102531392 137154421 1.3376822290679522 2.7951277408907194 chr16 90354753 164742835 1.8232890858547308 10.263544188346462 chr17 81195210 166094225 2.0456160529666714 8.602032061679449 chr18 78077248 116194698 1.4882017614145417 18.241660401331604 chr19 59128983 117584388 1.9886083276622566 19.20024526023516 chr20 63025520 119712636 1.8994311510638866 10.24410525888807 chr21 48129895 64200766 1.3339062135913655 14.659643643878782 chr22 51304566 78868058 1.5372522203969137 4.408189195586135 chrMT 16571 15299574 923.274032949128 248.13423347389903 chrX 155270560 111793592 0.7199921994227366 2.7544609595137324 chrY 59373566 61389212 1.0339485420161558 35.196020055953056